Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008814.1 Hibiscus syriacus cultivar Beakdansim tig00111976_pilon, whole genome shotgun sequence
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: 1021170
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:6603 original size:15 final size:17
Alignment explanation
Indices: 6567--6600 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
6557 TTTGATAACA
6567 TTTC-TATCTATTTCCT
1 TTTCTTATCTATTTCCT
6583 TTTCTTATC-ATTTCCT
1 TTTCTTATCTATTTCCT
6599 TT
1 TT
6601 CTTCTTTCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.12, C:0.24, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTATCTATTTCCT
Found at i:9033 original size:19 final size:20
Alignment explanation
Indices: 8999--9037 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 20
8989 TACATAAAAA
8999 ATACATGATTTTTTAATGAAG
1 ATACATGA-TTTTTAATGAAG
9020 ATACATGA-TTTTAATGAA
1 ATACATGATTTTTAATGAA
9038 AGTGCATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.05, G:0.13, T:0.41
Consensus pattern (20 bp):
ATACATGATTTTTAATGAAG
Found at i:9337 original size:16 final size:16
Alignment explanation
Indices: 9316--9357 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
9306 TGCCTAGAGA
9316 TGAACTAGGTTCAAGG
1 TGAACTAGGTTCAAGG
9332 TGAACTAGGTTCAAGG
1 TGAACTAGGTTCAAGG
*
9348 TGAGCTAGGT
1 TGAACTAGGT
9358 GAGTGTCTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.29, C:0.12, G:0.33, T:0.26
Consensus pattern (16 bp):
TGAACTAGGTTCAAGG
Found at i:10585 original size:19 final size:20
Alignment explanation
Indices: 10557--10596 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
10547 GAATAATAAT
10557 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
10577 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
10596 A
1 A
10597 AGAAATAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:11057 original size:19 final size:21
Alignment explanation
Indices: 11007--11058 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
10997 GAAATCCCTT
11007 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
*
11028 AGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
11047 TGAAGATACATG
1 TGAAAATACATG
11059 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.43
20 4 0.14
21 12 0.43
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:14496 original size:18 final size:18
Alignment explanation
Indices: 14427--14496 Score: 81
Period size: 19 Copynumber: 3.8 Consensus size: 18
14417 TTTCCTTGGC
14427 TTTCTTTCTCTTTTTGAAT
1 TTTCTTT-TCTTTTTGAAT
14446 TTTCTTTTTCTTTTAT-AAT
1 TTTC-TTTTCTTTT-TGAAT
**
14465 TTTC-TTTCTTTTTGTCT
1 TTTCTTTTCTTTTTGAAT
14482 TTTCTTTTCTTTTTG
1 TTTCTTTTCTTTTTG
14497 CACTCTAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 1 0.02
17 13 0.29
18 10 0.22
19 17 0.38
20 4 0.09
ACGTcount: A:0.07, C:0.14, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTCTTTTCTTTTTGAAT
Found at i:14792 original size:19 final size:20
Alignment explanation
Indices: 14764--14803 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
14754 GGAATATAAT
14764 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
14784 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
14803 A
1 A
14804 AGAAATGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:16774 original size:13 final size:13
Alignment explanation
Indices: 16756--16782 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
16746 TAATGTCAGC
16756 TTCTTCCGTATCT
1 TTCTTCCGTATCT
16769 TTCTTCCGTATCT
1 TTCTTCCGTATCT
16782 T
1 T
16783 CAGTGCTTAA
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:0.07, C:0.30, G:0.07, T:0.56
Consensus pattern (13 bp):
TTCTTCCGTATCT
Found at i:20030 original size:17 final size:16
Alignment explanation
Indices: 20008--20070 Score: 69
Period size: 18 Copynumber: 3.9 Consensus size: 16
19998 AAATTGGGGT
20008 ACAAAAAGAAAGAAAAG
1 ACAAAAAG-AAGAAAAG
20025 ACAAAAAGAAGAAAA-
1 ACAAAAAGAAGAAAAG
20040 ATTCAGAAAAGAAGAAAAG
1 A--CA-AAAAGAAGAAAAG
20059 --AAAAAGAAGAAA
1 ACAAAAAGAAGAAA
20071 TTCAAAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
14 11 0.26
15 2 0.05
16 7 0.17
17 10 0.24
18 12 0.29
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (16 bp):
ACAAAAAGAAGAAAAG
Found at i:20809 original size:24 final size:24
Alignment explanation
Indices: 20782--20834 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
20772 TCAAAACATC
*
20782 AAGAGATATGTCTTGT-GAATCACA
1 AAGAGACATGTCTTGTAG-ATCACA
*
20806 AAGAGACATGTCTTGTAGATCACG
1 AAGAGACATGTCTTGTAGATCACA
20830 AAGAG
1 AAGAG
20835 TCACGCCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 25 0.96
25 1 0.04
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.25
Consensus pattern (24 bp):
AAGAGACATGTCTTGTAGATCACA
Found at i:21629 original size:29 final size:30
Alignment explanation
Indices: 21597--21655 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
21587 CTTAGCTTTA
**
21597 TATTATGTTTACATATGTTTTAGAT-TCAT
1 TATTATGTTTACATATCATTTAGATATCAT
*
21626 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
21656 GGCAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.29, C:0.08, G:0.10, T:0.53
Consensus pattern (30 bp):
TATTATGTTTACATATCATTTAGATATCAT
Found at i:22553 original size:19 final size:21
Alignment explanation
Indices: 22529--22580 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
22519 CGGCCAAGAG
*
22529 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
22548 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
22569 CATGTATTTTCA
1 CATGTATTTTCA
22581 AAGGGGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:24346 original size:15 final size:14
Alignment explanation
Indices: 24302--24349 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 14
24292 TTGGAAATAA
24302 GAAATGAAAGAAAT
1 GAAATGAAAGAAAT
24316 GGAAATTGATAAGAAAT
1 -GAAA-TGA-AAGAAAT
24333 GAAATGGAAAGAAAT
1 GAAAT-GAAAGAAAT
24348 GA
1 GA
24350 TATCAAGGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 14 0.47
16 9 0.30
17 7 0.23
ACGTcount: A:0.58, C:0.00, G:0.25, T:0.17
Consensus pattern (14 bp):
GAAATGAAAGAAAT
Found at i:24346 original size:26 final size:24
Alignment explanation
Indices: 24298--24351 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 24
24288 TTAATTGGAA
24298 ATAAGAAATGAAAGAAATGGAAATTG
1 ATAAGAAATGAAAGAAA-GGAAA-TG
24324 ATAAGAAATGAAATGGAAA-GAAATG
1 ATAAGAAATGAAA--GAAAGGAAATG
24349 ATA
1 ATA
24352 TCAAGGTAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
25 5 0.19
26 17 0.65
28 4 0.15
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (24 bp):
ATAAGAAATGAAAGAAAGGAAATG
Found at i:29554 original size:24 final size:21
Alignment explanation
Indices: 29520--29562 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
29510 TCCACAAGAT
*
29520 ATGTCCTTTGACATTTCAAATG
1 ATGTCCTTTGA-AATTCAAATG
29542 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
29563 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAATG
Found at i:35216 original size:24 final size:21
Alignment explanation
Indices: 35181--35223 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
35171 GGCTCATTCT
*
35181 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
35204 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
35224 ATCTTGTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:36409 original size:15 final size:15
Alignment explanation
Indices: 36374--36402 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36364 GTGCTTCAAC
36374 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
36388 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
36403 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:41301 original size:13 final size:14
Alignment explanation
Indices: 41269--41307 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
41259 GATACTATCG
41269 TTCCATCACCATCT
1 TTCCATCACCATCT
41283 TTCCATCACCATC-
1 TTCCATCACCATCT
41296 TTCCATCACCAT
1 TTCCATCACCAT
41308 TGACGGCTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.23, C:0.44, G:0.00, T:0.33
Consensus pattern (14 bp):
TTCCATCACCATCT
Found at i:41500 original size:11 final size:11
Alignment explanation
Indices: 41484--41516 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
41474 CATTTTAATT
41484 CTTTCCATTTC
1 CTTTCCATTTC
41495 CTTTCCATTTC
1 CTTTCCATTTC
41506 CTTTCCATTTC
1 CTTTCCATTTC
41517 TTAATTCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.09, C:0.36, G:0.00, T:0.55
Consensus pattern (11 bp):
CTTTCCATTTC
Found at i:41505 original size:6 final size:6
Alignment explanation
Indices: 41485--41516 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
41475 ATTTTAATTC
41485 TTTCCA TTTCC- TTTCCA TTTCC- TTTCCA TTTC
1 TTTCCA TTTCCA TTTCCA TTTCCA TTTCCA TTTC
41517 TTAATTCTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 10 0.42
6 14 0.58
ACGTcount: A:0.09, C:0.34, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTCCA
Found at i:41798 original size:11 final size:11
Alignment explanation
Indices: 41778--41806 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
41768 AGTGCAAAAG
41778 AAAG-AAAGAA
1 AAAGAAAAGAA
41788 AAAGAAAAGAA
1 AAAGAAAAGAA
41799 AAAGAAAA
1 AAAGAAAA
41807 ATGAAGAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.22
11 14 0.78
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAGAAAAGAA
Found at i:41985 original size:17 final size:16
Alignment explanation
Indices: 41954--41990 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
41944 TTTCTTACTA
41954 TTTCATTTCTTTATTC
1 TTTCATTTCTTTATTC
*
41970 TTTCATTT-TTT-TTA
1 TTTCATTTCTTTATTC
41984 TTTCATT
1 TTTCATT
41991 ACCATATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 9 0.45
15 3 0.15
16 8 0.40
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCATTTCTTTATTC
Found at i:45762 original size:14 final size:14
Alignment explanation
Indices: 45743--45792 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 14
45733 CTTATAAGAT
*
45743 ACTATCGTTCCAGC
1 ACTATCTTTCCAGC
*
45757 ACTATCTTTCCATC
1 ACTATCTTTCCAGC
* *
45771 ACCATCTTTCCATC
1 ACTATCTTTCCAGC
*
45785 ACCATCTT
1 ACTATCTT
45793 CTATCACCAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.22, C:0.38, G:0.04, T:0.36
Consensus pattern (14 bp):
ACTATCTTTCCAGC
Found at i:45800 original size:13 final size:14
Alignment explanation
Indices: 45750--45801 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
45740 GATACTATCG
* *
45750 TTCCAGCACTATCT
1 TTCCATCACCATCT
45764 TTCCATCACCATCT
1 TTCCATCACCATCT
45778 TTCCATCACCATC-
1 TTCCATCACCATCT
*
45791 TTCTATCACCA
1 TTCCATCACCA
45802 GTCACGCCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
13 10 0.29
14 25 0.71
ACGTcount: A:0.23, C:0.40, G:0.02, T:0.35
Consensus pattern (14 bp):
TTCCATCACCATCT
Found at i:47011 original size:221 final size:221
Alignment explanation
Indices: 46618--47029 Score: 603
Period size: 221 Copynumber: 1.9 Consensus size: 221
46608 CCTGTGGAGT
* * * * *
46618 TGTTCAAATCATGTGTCATCGTTAAGATGGCGTCACGACTAAGGCTTTACTGGATGTATCATTTT
1 TGTTCAAATCATGTGTCATCATTAAGATGGCGTCACGACCAAGGATGTACTGGATGTAGCATTTT
* * *
46683 TGCAACAAATCTAAATCTTTGGTTTCTTCGAGATTGTATGTTTGACGATGTATGATGGAACCTTG
66 TGCAACAAATCTAAATCTTTGGTTTCTTCGAGATTATATGTTTGACGATGTATAATAGAACCTTG
* * *
46748 AATTAGATTGGTTTGGTGTTATTTTCCTCTTTCTAGTGGTAATAT-GTTAGGTGGATCACCTTAC
131 AATTAGATTAGTTTGGTGTTATTTTCCTCTTTCGAGTGGTAAT-TCATTAGGTGGATCACCTTAC
46812 ATCAGAATAGCCTTACATCAAAATGAG
195 ATCAGAATAGCCTTACATCAAAATGAG
* * * *
46839 TGTTCAAATCATGTTTCATCATTAAGATGGCTTCACGACCAAGGATGTCCTGGATGTAGCCTTTT
1 TGTTCAAATCATGTGTCATCATTAAGATGGCGTCACGACCAAGGATGTACTGGATGTAGCATTTT
* ** *
46904 TGTAACAAATCTAGCTCTTTGGTTTCTTTGAGATTATATGTTTGACGATGTATAATAGAACCTTG
66 TGCAACAAATCTAAATCTTTGGTTTCTTCGAGATTATATGTTTGACGATGTATAATAGAACCTTG
* *
46969 AATTAGATTAGTTTGGTGTTATTTTCCTATTTTCGA-TGGTAATTCATTATGTGGATCACCT
131 AATTAGATTAGTTTGGTGTTATTTTCCT-CTTTCGAGTGGTAATTCATTAGGTGGATCACCT
47030 AACACTTCTA
Statistics
Matches: 168, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
220 1 0.01
221 162 0.96
222 5 0.03
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.40
Consensus pattern (221 bp):
TGTTCAAATCATGTGTCATCATTAAGATGGCGTCACGACCAAGGATGTACTGGATGTAGCATTTT
TGCAACAAATCTAAATCTTTGGTTTCTTCGAGATTATATGTTTGACGATGTATAATAGAACCTTG
AATTAGATTAGTTTGGTGTTATTTTCCTCTTTCGAGTGGTAATTCATTAGGTGGATCACCTTACA
TCAGAATAGCCTTACATCAAAATGAG
Found at i:48674 original size:13 final size:14
Alignment explanation
Indices: 48647--48682 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
48637 ACTATCGTTT
48647 CATCACCATCTTTC
1 CATCACCATCTTTC
48661 CATCACCATC-TTC
1 CATCACCATCTTTC
48674 CATCACCAT
1 CATCACCAT
48683 TCACGCCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.25, C:0.44, G:0.00, T:0.31
Consensus pattern (14 bp):
CATCACCATCTTTC
Found at i:49330 original size:16 final size:17
Alignment explanation
Indices: 49311--49345 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
49301 TTCTTACTAT
49311 TTCATTTCTTTA-TTCA
1 TTCATTTCTTTATTTCA
*
49327 TTCATTTTTTTATTTCA
1 TTCATTTCTTTATTTCA
49344 TT
1 TT
49346 ACCATATCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.17, C:0.14, G:0.00, T:0.69
Consensus pattern (17 bp):
TTCATTTCTTTATTTCA
Found at i:55658 original size:15 final size:16
Alignment explanation
Indices: 55618--55660 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
55608 AAAGTTTTAA
*
55618 TATAGTTATTTTCATC
1 TATAGTTATTATCATC
55634 TATA-TATATTAT-ATC
1 TATAGT-TATTATCATC
55649 TATAGTTATTAT
1 TATAGTTATTAT
55661 GATGATAACT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 14 0.58
16 10 0.42
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.56
Consensus pattern (16 bp):
TATAGTTATTATCATC
Found at i:56884 original size:26 final size:26
Alignment explanation
Indices: 56819--56886 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 26
56809 ATGAACCCAC
* * *
56819 ATGCAAGGCACATAGGGGTTGGTCAT
1 ATGCAAGGCACATGGGGGCTGATCAT
56845 ATGCAAGGCACATGGGGGCTGATCAT
1 ATGCAAGGCACATGGGGGCTGATCAT
*
56871 ATGCAAAGCACATGGG
1 ATGCAAGGCACATGGG
56887 TGTTCTAGGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.29, C:0.18, G:0.34, T:0.19
Consensus pattern (26 bp):
ATGCAAGGCACATGGGGGCTGATCAT
Found at i:58709 original size:22 final size:21
Alignment explanation
Indices: 58670--58710 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
58660 CCATCTCCAT
*
58670 TTCATCATCAACATCATCAAC
1 TTCATCATCAACACCATCAAC
*
58691 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
58711 GTTCCACAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.37, C:0.34, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCAAC
Found at i:61859 original size:12 final size:12
Alignment explanation
Indices: 61833--61866 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
61823 AAGGTGATTC
*
61833 AATGGTGAT-GA
1 AATGGTAATGGA
61844 AATGGTAATGGA
1 AATGGTAATGGA
61856 AATGGTAATGG
1 AATGGTAATGG
61867 TGTTGGTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 8 0.38
12 13 0.62
ACGTcount: A:0.38, C:0.00, G:0.35, T:0.26
Consensus pattern (12 bp):
AATGGTAATGGA
Found at i:62074 original size:19 final size:20
Alignment explanation
Indices: 62035--62085 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
62025 GGAACCCCTT
62035 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
*
62056 TGAAGATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
62075 TGAAAGTACAT
1 TGAAAATACAT
62086 CCTTTTGGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 15 0.56
21 12 0.44
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:62091 original size:19 final size:19
Alignment explanation
Indices: 62050--62091 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
62040 ATACATGATT
*
62050 TTTTAATGAAGATACATGA
1 TTTTAATGAAGATACATCA
*
62069 TTTTAATGAA-AGTACATCC
1 TTTTAATGAAGA-TACATCA
62088 TTTT
1 TTTT
62092 GGCCAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.43
Consensus pattern (19 bp):
TTTTAATGAAGATACATCA
Found at i:64401 original size:13 final size:13
Alignment explanation
Indices: 64383--64409 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
64373 ATTTTGTTCG
64383 AACAAATTAAGCA
1 AACAAATTAAGCA
64396 AACAAATTAAGCA
1 AACAAATTAAGCA
64409 A
1 A
64410 TGTGTGATGT
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:0.63, C:0.15, G:0.07, T:0.15
Consensus pattern (13 bp):
AACAAATTAAGCA
Found at i:64768 original size:21 final size:21
Alignment explanation
Indices: 64744--64789 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
64734 AGAGAATGAC
*
64744 GATGATATAGGCGTGAATGGT
1 GATGATATAGACGTGAATGGT
64765 GATGATATAGACGTGAATGGT
1 GATGATATAGACGTGAATGGT
64786 GATG
1 GATG
64790 GAATGATAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.04, G:0.37, T:0.28
Consensus pattern (21 bp):
GATGATATAGACGTGAATGGT
Found at i:69961 original size:15 final size:15
Alignment explanation
Indices: 69897--69968 Score: 62
Period size: 15 Copynumber: 4.9 Consensus size: 15
69887 GCAAAATTAA
69897 AAGAAA-GAAATGATT
1 AAGAAAGGAAATGA-T
*
69912 AAG-ATGGAAAT-AT
1 AAGAAAGGAAATGAT
* *
69925 AA-AAAAGAAATAGAAG
1 AAGAAAGGAAAT-G-AT
69941 AAGAAAGGAAATGAT
1 AAGAAAGGAAATGAT
69956 AAGAAAGGAAATG
1 AAGAAAGGAAATG
69969 GAAATAAATG
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
13 9 0.20
14 2 0.04
15 22 0.49
16 4 0.09
17 8 0.18
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (15 bp):
AAGAAAGGAAATGAT
Found at i:82758 original size:36 final size:35
Alignment explanation
Indices: 82663--82776 Score: 165
Period size: 35 Copynumber: 3.2 Consensus size: 35
82653 GGGATTGGTG
*
82663 GTTATAGGCGTGAAATGGTGATAGAAGATGGTGAT
1 GTTATAGGCGTGAAATGGTGATGGAAGATGGTGAT
* * * *
82698 GATATAGGTGTGCAATGGTGATGGAAGATGGTGAA
1 GTTATAGGCGTGAAATGGTGATGGAAGATGGTGAT
*
82733 GTTATAGGCATGAAAATGGTGATGGAAGATGGTGAT
1 GTTATAGGCGTG-AAATGGTGATGGAAGATGGTGAT
82769 GTTATAGG
1 GTTATAGG
82777 TAGTAGCTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 39 0.57
36 29 0.43
ACGTcount: A:0.32, C:0.03, G:0.38, T:0.28
Consensus pattern (35 bp):
GTTATAGGCGTGAAATGGTGATGGAAGATGGTGAT
Found at i:87929 original size:592 final size:592
Alignment explanation
Indices: 86805--87988 Score: 2359
Period size: 592 Copynumber: 2.0 Consensus size: 592
86795 AGAAAGGGAG
86805 GATGATACATGCATCACAAGGTTCACATCAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACT
1 GATGATACATGCATCACAAGGTTCACATCAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACT
86870 CGTCCAAGCTTTGGAAAAGAAGATCAGAACAGCAGCGCACTTGAGACGACTTTTTGAATGGGATC
66 CGTCCAAGCTTTGGAAAAGAAGATCAGAACAGCAGCGCACTTGAGACGACTTTTTGAATGGGATC
86935 CTGATATTATTTGGTCGACATGTCTTCTGGAGATACAACCGTCTGTCTCTTATCTTTCTAACGGT
131 CTGATATTATTTGGTCGACATGTCTTCTGGAGATACAACCGTCTGTCTCTTATCTTTCTAACGGT
87000 TCTTGAATCGCATCAATCCGATATCGGAAACTCAAGATATGGTCATTTTACTGAAGACGGTGCAT
196 TCTTGAATCGCATCAATCCGATATCGGAAACTCAAGATATGGTCATTTTACTGAAGACGGTGCAT
87065 GCAGGAAATCCTATACGGGATTAATACGTTATTTTGTAAATATTACGAATTTTCAATATTTATAT
261 GCAGGAAATCCTATACGGGATTAATACGTTATTTTGTAAATATTACGAATTTTCAATATTTATAT
87130 TGATTATTTGTAATATAATTTAATATAGGATGATTAATTATCTTTTAGGATCAGATTTATTATTT
326 TGATTATTTGTAATATAATTTAATATAGGATGATTAATTATCTTTTAGGATCAGATTTATTATTT
87195 TATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTATTATTATTTTATTAGGAATTAGGG
391 TATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTATTATTATTTTATTAGGAATTAGGG
87260 TTAAAACATGTTTAGTTTATTAATATTTTATTCTTTAGTTATTTAGGACCTTTAGAATTCAGCCC
456 TTAAAACATGTTTAGTTTATTAATATTTTATTCTTTAGTTATTTAGGACCTTTAGAATTCAGCCC
87325 CTATATAAAGGAGGCTTCATTCAACTTTGTAAAGCAGATTTCTTTGATTAATAATACAACGAGAG
521 CTATATAAAGGAGGCTTCATTCAACTTTGTAAAGCAGATTTCTTTGATTAATAATACAACGAGAG
87390 TTCGTTT
586 TTCGTTT
87397 GATGATACATGCATCACAAGGTTCACATCAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACT
1 GATGATACATGCATCACAAGGTTCACATCAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACT
87462 CGTCCAAGCTTTGGAAAAGAAGATCAGAACAGCAGCGCACTTGAGACGACTTTTTGAATGGGATC
66 CGTCCAAGCTTTGGAAAAGAAGATCAGAACAGCAGCGCACTTGAGACGACTTTTTGAATGGGATC
87527 CTGATATTATTTGGTCGACATGTCTTCTGGAGATACAACCGTCTGTCTCTTATCTTTCTAACGGT
131 CTGATATTATTTGGTCGACATGTCTTCTGGAGATACAACCGTCTGTCTCTTATCTTTCTAACGGT
*
87592 TCTTGAATCGCATCAATCCGATATCGGGAACTCAAGATATGGTCATTTTACTGAAGACGGTGCAT
196 TCTTGAATCGCATCAATCCGATATCGGAAACTCAAGATATGGTCATTTTACTGAAGACGGTGCAT
87657 GCAGGAAATCCTATACGGGATTAATACGTTATTTTGTAAATATTACGAATTTTCAATATTTATAT
261 GCAGGAAATCCTATACGGGATTAATACGTTATTTTGTAAATATTACGAATTTTCAATATTTATAT
87722 TGATTATTTGTAATATAATTTAATATAGGATGATTAATTATCTTTTAGGATCAGATTTATTATTT
326 TGATTATTTGTAATATAATTTAATATAGGATGATTAATTATCTTTTAGGATCAGATTTATTATTT
87787 TATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTATTATTATTTTATTAGGAATTAGGG
391 TATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTATTATTATTTTATTAGGAATTAGGG
87852 TTAAAACATGTTTAGTTTATTAATATTTTATTCTTTAGTTATTTAGGACCTTTAGAATTCAGCCC
456 TTAAAACATGTTTAGTTTATTAATATTTTATTCTTTAGTTATTTAGGACCTTTAGAATTCAGCCC
87917 CTATATAAAGGAGGCTTCATTCAACTTTGTAAAGCAGATTTCTTTGATTAATAATACAACGAGAG
521 CTATATAAAGGAGGCTTCATTCAACTTTGTAAAGCAGATTTCTTTGATTAATAATACAACGAGAG
87982 TTCGTTT
586 TTCGTTT
87989 TTGCAAGTGC
Statistics
Matches: 591, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
592 591 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (592 bp):
GATGATACATGCATCACAAGGTTCACATCAAAGGAAGAAGTAATAACTCTTCCAAATGATCCACT
CGTCCAAGCTTTGGAAAAGAAGATCAGAACAGCAGCGCACTTGAGACGACTTTTTGAATGGGATC
CTGATATTATTTGGTCGACATGTCTTCTGGAGATACAACCGTCTGTCTCTTATCTTTCTAACGGT
TCTTGAATCGCATCAATCCGATATCGGAAACTCAAGATATGGTCATTTTACTGAAGACGGTGCAT
GCAGGAAATCCTATACGGGATTAATACGTTATTTTGTAAATATTACGAATTTTCAATATTTATAT
TGATTATTTGTAATATAATTTAATATAGGATGATTAATTATCTTTTAGGATCAGATTTATTATTT
TATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAGTTATTATTATTTTATTAGGAATTAGGG
TTAAAACATGTTTAGTTTATTAATATTTTATTCTTTAGTTATTTAGGACCTTTAGAATTCAGCCC
CTATATAAAGGAGGCTTCATTCAACTTTGTAAAGCAGATTTCTTTGATTAATAATACAACGAGAG
TTCGTTT
Found at i:96188 original size:35 final size:35
Alignment explanation
Indices: 96148--96217 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
96138 ATTGATGGTT
*
96148 ATATAGGCGTGAAATGGTGATAGAATATGGTGATG
1 ATATAGGCGTGAAATGGTGATAGAAAATGGTGATG
* *
96183 ATATAGGCGTGTAATGGTGATGGAAAATGGTGATG
1 ATATAGGCGTGAAATGGTGATAGAAAATGGTGATG
96218 GAAGATGAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.36, T:0.29
Consensus pattern (35 bp):
ATATAGGCGTGAAATGGTGATAGAAAATGGTGATG
Found at i:96213 original size:13 final size:13
Alignment explanation
Indices: 96195--96220 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
96185 ATAGGCGTGT
96195 AATGGTGATGGAA
1 AATGGTGATGGAA
96208 AATGGTGATGGAA
1 AATGGTGATGGAA
96221 GATGAGGTAG
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:0.00, G:0.38, T:0.23
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:98650 original size:10 final size:9
Alignment explanation
Indices: 98631--98683 Score: 61
Period size: 9 Copynumber: 5.7 Consensus size: 9
98621 AAATTTTGGC
98631 TTTTTTGTT
1 TTTTTTGTT
98640 TTTTATTGTT
1 TTTT-TTGTT
**
98650 TTTTTTGCC
1 TTTTTTGTT
*
98659 TTTCTTGTT
1 TTTTTTGTT
98668 TTTTTTGGTT
1 TTTTTT-GTT
98678 TTTTTT
1 TTTTTT
98684 AAAAATAGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
9 18 0.50
10 18 0.50
ACGTcount: A:0.02, C:0.06, G:0.11, T:0.81
Consensus pattern (9 bp):
TTTTTTGTT
Found at i:98661 original size:28 final size:28
Alignment explanation
Indices: 98624--98683 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
98614 ATTTTTGAAA
* *
98624 TTTTGGCTTTTTTGTTTTTTATT-GTTTT
1 TTTTGCCTTTCTTGTTTTTT-TTGGTTTT
98652 TTTTGCCTTTCTTGTTTTTTTTGGTTTT
1 TTTTGCCTTTCTTGTTTTTTTTGGTTTT
98680 TTTT
1 TTTT
98684 AAAAATAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.02, C:0.07, G:0.13, T:0.78
Consensus pattern (28 bp):
TTTTGCCTTTCTTGTTTTTTTTGGTTTT
Found at i:108955 original size:11 final size:13
Alignment explanation
Indices: 108923--108957 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
108913 TGGCCAAAGA
108923 TGAAAAGGTATGT
1 TGAAAAGGTATGT
108936 TGAAAAGGTATG-
1 TGAAAAGGTATGT
108948 TG-AAAGGTAT
1 TGAAAAGGTAT
108958 TTAGTATGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
12 2 0.09
13 12 0.55
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:113804 original size:14 final size:14
Alignment explanation
Indices: 113780--113856 Score: 54
Period size: 14 Copynumber: 5.5 Consensus size: 14
113770 CAATTCCTTG
113780 TTGCA-TTTGCATC
1 TTGCATTTTGCATC
113793 TTGCATTTTGCA-C
1 TTGCATTTTGCATC
** *
113806 TCCCATTTTTGCATAT
1 TTGCA-TTTTGCAT-C
113822 TTGCA-TTTGCAT-
1 TTGCATTTTGCATC
*
113834 GTGCATCTTTGCATC
1 TTGCAT-TTTGCATC
113849 TTTGCATT
1 -TTGCATT
113857 AGTATATATA
Statistics
Matches: 49, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
12 4 0.08
13 9 0.18
14 27 0.55
15 1 0.02
16 8 0.16
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (14 bp):
TTGCATTTTGCATC
Found at i:115257 original size:12 final size:12
Alignment explanation
Indices: 115242--115304 Score: 63
Period size: 12 Copynumber: 5.1 Consensus size: 12
115232 AAAAAGAGAT
*
115242 AAAAGAAAGCAA
1 AAAAGAAAACAA
115254 AAAAGGAAAACAA
1 AAAA-GAAAACAA
* *
115267 TAGAGAAAACAA
1 AAAAGAAAACAA
* *
115279 AACAAAAAAAGAA
1 AA-AAGAAAACAA
115292 AAAAGAAAACAA
1 AAAAGAAAACAA
115304 A
1 A
115305 TCCAATATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
12 22 0.55
13 18 0.45
ACGTcount: A:0.78, C:0.08, G:0.13, T:0.02
Consensus pattern (12 bp):
AAAAGAAAACAA
Found at i:115285 original size:30 final size:30
Alignment explanation
Indices: 115228--115295 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
115218 GAGAGTAAAG
* * *
115228 GGAAAAAAAGAGATAAAAGAAAGCAAAAAA
1 GGAAAAAAAGAGAGAAAACAAAACAAAAAA
* *
115258 GGAAAACAATAGAGAAAACAAAACAAAAAA
1 GGAAAAAAAGAGAGAAAACAAAACAAAAAA
*
115288 AGAAAAAA
1 GGAAAAAA
115296 GAAAACAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.75, C:0.06, G:0.16, T:0.03
Consensus pattern (30 bp):
GGAAAAAAAGAGAGAAAACAAAACAAAAAA
Found at i:117322 original size:54 final size:53
Alignment explanation
Indices: 117180--117458 Score: 171
Period size: 54 Copynumber: 5.2 Consensus size: 53
117170 CCCAATGAAC
* * * **
117180 ATGATGTTTTCTAAAGAAGTTTTAAAGAAA-CTAAGTATAATTTTCAGGGGTTTCT
1 ATGATGATTTCCAAAGAA-TTTTTAAGAAAGCTAAGCCTAATTTTCA-GGGTTT-T
* * * *
117235 -TGAT-ATATT-CAAATGAGTTATTAA-ATAAACTAAGCCTGATTTTCAGGGTTTT
1 ATGATGAT-TTCCAAA-GAATTTTTAAGA-AAGCTAAGCCTAATTTTCAGGGTTTT
* **
117287 ATGATGATTTCCAAAGAATTTTTAAGAGAAGCTAAGACTAATTTTTGGGGTTTT
1 ATGATGATTTCCAAAGAATTTTTAAGA-AAGCTAAGCCTAATTTTCAGGGTTTT
* * * *
117341 TTGAT-ATTTTCAAATGAGTTTTT-AGAAA-CTAAGCCTGATTTTCAAGGGTTTCTT
1 ATGATGATTTCCAAA-GAATTTTTAAGAAAGCTAAGCCTAATTTTC-AGGG-TT-TT
* * * * *
117395 GATGATTATTTCTAAAGAATTTTTAAAAAAAGCAAAGCCTAATTTTTAGGGGTTTCT
1 -ATGATGATTTCCAAAGAATTTTT-AAGAAAGCTAAGCCTAATTTTCA-GGGTTT-T
117452 -TGATGAT
1 ATGATGAT
117459 AATTGAACAG
Statistics
Matches: 173, Mismatches: 32, Indels: 38
0.71 0.13 0.16
Matches are distributed among these distances:
51 12 0.07
52 7 0.04
53 44 0.25
54 62 0.36
55 17 0.10
56 8 0.05
57 8 0.05
58 15 0.09
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.41
Consensus pattern (53 bp):
ATGATGATTTCCAAAGAATTTTTAAGAAAGCTAAGCCTAATTTTCAGGGTTTT
Found at i:117993 original size:8 final size:8
Alignment explanation
Indices: 117980--118022 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
117970 TCTTCTTTTT
117980 AAATGAAA
1 AAATGAAA
117988 AAATGAAA
1 AAATGAAA
117996 AAATGTAAA
1 AAATG-AAA
118005 AAA-G-AA
1 AAATGAAA
118011 AAA-GAAA
1 AAATGAAA
118018 AAATG
1 AAATG
118023 GTACTTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 6 0.19
7 5 0.16
8 15 0.47
9 6 0.19
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (8 bp):
AAATGAAA
Found at i:118796 original size:16 final size:16
Alignment explanation
Indices: 118775--118811 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
118765 TAACTCGATA
118775 TTTTAGTCCTTTAACC
1 TTTTAGTCCTTTAACC
118791 TTTTAGTCCTTTAACC
1 TTTTAGTCCTTTAACC
118807 TTTTA
1 TTTTA
118812 TTCCCCAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.19, C:0.22, G:0.05, T:0.54
Consensus pattern (16 bp):
TTTTAGTCCTTTAACC
Found at i:124764 original size:17 final size:17
Alignment explanation
Indices: 124741--124782 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
124731 TATTTTCTTT
124741 ATTTTTACT-TTAAATC
1 ATTTTTACTATTAAATC
* *
124757 ACTTTTTATTATTTAATC
1 A-TTTTTACTATTAAATC
124775 ATTTTTAC
1 ATTTTTAC
124783 CAAAACCTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
16 1 0.05
17 13 0.62
18 7 0.33
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.60
Consensus pattern (17 bp):
ATTTTTACTATTAAATC
Found at i:138501 original size:22 final size:22
Alignment explanation
Indices: 138476--138518 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
138466 AACAATAGAG
*
138476 GGTCTAAATTATTTTTCAGATA
1 GGTCTAAATTATTTCTCAGATA
138498 GGTCTAAATTATTTCTCAGAT
1 GGTCTAAATTATTTCTCAGAT
138519 GTACTTGGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (22 bp):
GGTCTAAATTATTTCTCAGATA
Found at i:142423 original size:11 final size:11
Alignment explanation
Indices: 142399--142443 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
142389 TTGGTGCTGG
142399 AAACAAGATAA
1 AAACAAGATAA
* *
142410 AAATAAGATTA
1 AAACAAGATAA
142421 AAACAAGATAA
1 AAACAAGATAA
142432 AGAA-AAGATAA
1 A-AACAAGATAA
142443 A
1 A
142444 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:142427 original size:22 final size:22
Alignment explanation
Indices: 142399--142440 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
142389 TTGGTGCTGG
142399 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
142421 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
142441 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:146763 original size:8 final size:8
Alignment explanation
Indices: 146752--146801 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
146742 AAATTTTGGC
146752 TTTTTTTG
1 TTTTTTTG
146760 TTTTTTTG
1 TTTTTTTG
146768 ---TTTT-
1 TTTTTTTG
146772 TTTTTTTG
1 TTTTTTTG
*
146780 CCTTTTTTG
1 -TTTTTTTG
146789 TTTTTTTG
1 TTTTTTTG
146797 TTTTT
1 TTTTT
146802 GAAAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
5 4 0.11
7 4 0.11
8 20 0.57
9 7 0.20
ACGTcount: A:0.00, C:0.04, G:0.10, T:0.86
Consensus pattern (8 bp):
TTTTTTTG
Found at i:146777 original size:29 final size:29
Alignment explanation
Indices: 146745--146801 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
146735 TTTTTTGAAA
*
146745 TTTTGGCTTTTTTTGTTTTTTTGTTTTTT
1 TTTTGGCCTTTTTTGTTTTTTTGTTTTTT
*
146774 TTTTTGCCTTTTTTGTTTTTTTGTTTTT
1 TTTTGGCCTTTTTTGTTTTTTTGTTTTT
146802 GAAAAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.82
Consensus pattern (29 bp):
TTTTGGCCTTTTTTGTTTTTTTGTTTTTT
Found at i:147144 original size:11 final size:11
Alignment explanation
Indices: 147120--147164 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
147110 TTGGTGCTGG
147120 AAACAAGATAA
1 AAACAAGATAA
* *
147131 AAATAAGATTA
1 AAACAAGATAA
147142 AAACAAGATAA
1 AAACAAGATAA
147153 AGAA-AAGATAA
1 A-AACAAGATAA
147164 A
1 A
147165 TGAATTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 27 0.93
12 2 0.07
ACGTcount: A:0.71, C:0.04, G:0.11, T:0.13
Consensus pattern (11 bp):
AAACAAGATAA
Found at i:147148 original size:22 final size:22
Alignment explanation
Indices: 147120--147161 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
147110 TTGGTGCTGG
147120 AAACAAGATAAA-AATAAGATTA
1 AAACAAGATAAAGAA-AAGATTA
147142 AAACAAGATAAAGAAAAGAT
1 AAACAAGATAAAGAAAAGAT
147162 AAATGAATTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.69, C:0.05, G:0.12, T:0.14
Consensus pattern (22 bp):
AAACAAGATAAAGAAAAGATTA
Found at i:148972 original size:32 final size:31
Alignment explanation
Indices: 148936--148996 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
148926 TCTTACATGT
*
148936 ACTAACTAATGTCTTTTCTTTTGTTTGTGTAC
1 ACTAACTAATGTCTTCTCTTTT-TTTGTGTAC
* *
148968 ACTAACTTATTTCTTCTCTTTTTTTGTGT
1 ACTAACTAATGTCTTCTCTTTTTTTGTGT
148997 CATTTTGTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 7 0.27
32 19 0.73
ACGTcount: A:0.16, C:0.16, G:0.10, T:0.57
Consensus pattern (31 bp):
ACTAACTAATGTCTTCTCTTTTTTTGTGTAC
Found at i:149533 original size:27 final size:27
Alignment explanation
Indices: 149503--149570 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
149493 GGATCAATAT
149503 TTTTGCATATGCATTTGCATCTTT-GCA
1 TTTTGCATATGCATTT-CATCTTTAGCA
*
149530 TTTTGCATATGCATTTCATTTTTAAGCA
1 TTTTGCATATGCATTTCATCTTT-AGCA
*
149558 TTTT-CACATGCAT
1 TTTTGCATATGCAT
149571 CATTCATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
26 6 0.16
27 24 0.65
28 7 0.19
ACGTcount: A:0.22, C:0.18, G:0.12, T:0.49
Consensus pattern (27 bp):
TTTTGCATATGCATTTCATCTTTAGCA
Found at i:150912 original size:31 final size:31
Alignment explanation
Indices: 150874--150993 Score: 90
Period size: 31 Copynumber: 3.9 Consensus size: 31
150864 AGAAAAATCG
*
150874 AAGAAAAAAACAAAGAGCAAAGAGAAGAA-AA
1 AAGAAAAAAACAAAGAGCAAA-AGAAAAACAA
*
150905 AAG-AAAAAA-AAAGAGGAAAAGAAAAAGCAA
1 AAGAAAAAAACAAAGAGCAAAAGAAAAA-CAA
* *
150935 AGAGAAAAAAAACAAAGAGAAAAAGTAAAGA-AA
1 A-AG-AAAAAAACAAAGAGCAAAAG-AAAAACAA
* * *
150968 AAGAACAAAAGAAA-AAC-AAAGAAAAA
1 AAGAAAAAAACAAAGAGCAAAAGAAAAA
150994 GAGATGACAA
Statistics
Matches: 73, Mismatches: 9, Indels: 17
0.74 0.09 0.17
Matches are distributed among these distances:
28 10 0.14
29 13 0.18
30 10 0.14
31 14 0.19
32 2 0.03
33 9 0.12
34 11 0.15
35 4 0.05
ACGTcount: A:0.77, C:0.05, G:0.17, T:0.01
Consensus pattern (31 bp):
AAGAAAAAAACAAAGAGCAAAAGAAAAACAA
Found at i:150930 original size:6 final size:6
Alignment explanation
Indices: 150902--150995 Score: 56
Period size: 6 Copynumber: 16.2 Consensus size: 6
150892 AAAGAGAAGA
* * * *
150902 AAAAAG AAAAA- AAAAGAG GAAAAG AAAAAG -CAAAG AGAAA- AAAAAC
1 AAAAAG AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
* * *
150948 AAAGAG AAAAAG -TAAAG AAAAAG AACAAA- AGAAAA- ACAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG A-AAAAG AAAAAG AAAAAG
150995 A
1 A
150996 GATGACAAAA
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
5 19 0.28
6 42 0.62
7 7 0.10
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:150934 original size:41 final size:38
Alignment explanation
Indices: 150880--150993 Score: 113
Period size: 41 Copynumber: 2.8 Consensus size: 38
150870 ATCGAAGAAA
* *
150880 AAAACAAAGAGCAAAGAGAAGAAAAAAGAAAAAAAAAGAGG
1 AAAAGAAAAAGCAAAGAGAA-AAAAAAGAAAAAAAAA-A-G
* *
150921 AAAAGAAAAAGCAAAGAGAAAAAAAACAAAGAGAAAAAG
1 AAAAGAAAAAGCAAAGAGAAAAAAAAGAAA-AAAAAAAG
*
150960 TAAAGAAAAAGAACAAA-AGAAAAACAAAGAAAAA
1 AAAAGAAAAAG--CAAAGAGAAAAA-AAAGAAAAA
150994 GAGATGACAA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
39 11 0.18
40 18 0.29
41 33 0.53
ACGTcount: A:0.76, C:0.05, G:0.18, T:0.01
Consensus pattern (38 bp):
AAAAGAAAAAGCAAAGAGAAAAAAAAGAAAAAAAAAAG
Found at i:150944 original size:15 final size:15
Alignment explanation
Indices: 150877--150958 Score: 64
Period size: 15 Copynumber: 5.3 Consensus size: 15
150867 AAAATCGAAG
150877 AAAAAAACAAAGAGCA
1 AAAAAAACAAAGAG-A
150893 AAGAGAAGAA-AAA-AGA
1 AA-A-AA-AACAAAGAGA
*
150909 AAAAAAA-AGAG-GAA
1 AAAAAAACAAAGAG-A
150923 AAGAAAAAGCAAAGAGA
1 AA-AAAAA-CAAAGAGA
150940 AAAAAAACAAAGAGA
1 AAAAAAACAAAGAGA
150955 AAAA
1 AAAA
150959 GTAAAGAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
13 5 0.09
14 5 0.09
15 18 0.33
16 10 0.18
17 9 0.16
18 6 0.11
19 2 0.04
ACGTcount: A:0.77, C:0.05, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAAAACAAAGAGA
Found at i:150957 original size:13 final size:13
Alignment explanation
Indices: 150924--150993 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
150914 AAAGAGGAAA
*
150924 AGAAAAAGCAAAG
1 AGAAAAAACAAAG
150937 AGAAAAAAAACAAAG
1 AG--AAAAAACAAAG
**
150952 AGAAAAAGTAAAG
1 AGAAAAAACAAAG
150965 A-AAAAGAACAAA-
1 AGAAAA-AACAAAG
150977 AG-AAAAACAAAG
1 AGAAAAAACAAAG
150989 A-AAAA
1 AGAAAA
150994 GAGATGACAA
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
11 6 0.13
12 12 0.26
13 16 0.35
15 12 0.26
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.01
Consensus pattern (13 bp):
AGAAAAAACAAAG
Found at i:150971 original size:34 final size:33
Alignment explanation
Indices: 150877--150993 Score: 95
Period size: 34 Copynumber: 3.5 Consensus size: 33
150867 AAAATCGAAG
*
150877 AAAAAAACAAAGAG-CAAAGAGAAGAAAAA-AG-
1 AAAAAAACAAAGAGAAAAAGA-AAGAAAAAGAGA
*
150908 -AAAAAA-AAAGAGGAAAAGAAA-AAGCAAAGAGA
1 AAAAAAACAAAGAGAAAAAGAAAGAA--AAAGAGA
*
150940 AAAAAAACAAAGAGAAAAAGTAAAGAAAAAGAACAA
1 AAAAAAACAAAGAGAAAAAG-AAAGAAAAAG-A-GA
150976 AAGAAAAACAAAGA-AAAA
1 AA-AAAAACAAAGAGAAAA
150994 GAGATGACAA
Statistics
Matches: 71, Mismatches: 3, Indels: 19
0.76 0.03 0.20
Matches are distributed among these distances:
28 2 0.03
29 8 0.11
30 14 0.20
31 2 0.03
33 6 0.08
34 15 0.21
35 4 0.06
36 9 0.13
37 11 0.15
ACGTcount: A:0.77, C:0.05, G:0.17, T:0.01
Consensus pattern (33 bp):
AAAAAAACAAAGAGAAAAAGAAAGAAAAAGAGA
Found at i:152633 original size:130 final size:130
Alignment explanation
Indices: 152393--152758 Score: 450
Period size: 130 Copynumber: 2.8 Consensus size: 130
152383 CCAAAATCCC
* * * * * *
152393 TTCCTAAAGATGGCATGTCATCCTCATCACGTGGGAACCGTGTCATCCCCCGACCAGATCTCCTC
1 TTCCTAAAGACGGCATGACATCTTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTC
* * * ** * *
152458 ATCATGTATGAGCCGTGTCACCCCTGATAACCAATTATCCTCATCATATAGGGATCGTGTTATCA
66 ATCACGTAGGAGCTGTGTCACCCCTGATAACCAATCGTCCACATCATATAGGAATCGTGTTATCA
* ** *
152523 TTCCTAAAGACGGCCA-G-CTGTCTTCATCGTGTAGGAATCATGTCATCCCCCGACCAGACCTCC
1 TTCCTAAAGACGG-CATGAC-ATCTTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCC
* *
152586 TCATCACGTAGGAGCTGTGTCACCCCTGATAACCAATCGTCCACATCATGTAGGAATTGTGTTAT
64 TCATCACGTAGGAGCTGTGTCACCCCTGATAACCAATCGTCCACATCATATAGGAATCGTGTTAT
152651 CA
129 CA
* * * *
152653 TTCCTAAAGATGGCATGACATCTTCATCACGTAGGAACCGTGTCATCCCCTGACCAAACCTCCTC
1 TTCCTAAAGACGGCATGACATCTTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTC
* *
152718 ATCACGTAGGAG-TCGTGTCATCCCTAGATAACCAGTCGTCC
66 ATCACGTAGGAGCT-GTGTCACCCCT-GATAACCAATCGTCC
152759 TCCGAGTTAT
Statistics
Matches: 202, Mismatches: 28, Indels: 11
0.84 0.12 0.05
Matches are distributed among these distances:
129 4 0.02
130 181 0.90
131 17 0.08
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (130 bp):
TTCCTAAAGACGGCATGACATCTTCATCACGTAGGAACCATGTCATCCCCCGACCAGACCTCCTC
ATCACGTAGGAGCTGTGTCACCCCTGATAACCAATCGTCCACATCATATAGGAATCGTGTTATCA
Found at i:152873 original size:121 final size:121
Alignment explanation
Indices: 152653--152873 Score: 288
Period size: 121 Copynumber: 1.8 Consensus size: 121
152643 TGTGTTATCA
152653 TTCCTAAAGATGGCATGACATCTTCATCACGTAGGAACCGTGTCATCCCCTGACCAAACCTCCTC
1 TTCCTAAAGATGGCATGACATCTTCATCACGTAGGAACCGTGTCATCCCCTGACCAAACCTCCTC
* *
152718 ATCACGTAGGAGTCGTGTCATCCCTAGATAACCAGTCGTCCTCCGAGTTATCACTC
66 ATCACGTAGCAGTCGTGTCATCCCTAGACAACCAGTCGTCCTCCGAGTTATCACTC
* * * * * *
152774 TTCCTAAAGATGGCCA-GACCTCTTTATCACGTATGAGCCGTGTCATCCACC-GACCATATCTCC
1 TTCCTAAAGATGG-CATGACATCTTCATCACGTAGGAACCGTGTCATCC-CCTGACCAAACCTCC
* *
152837 TCATCGCGTAGCAG-CTGTGTCA-CCCTTAGACGACCAG
64 TCATCACGTAGCAGTC-GTGTCATCCC-TAGACAACCAG
152874 ACCTCTTTAT
Statistics
Matches: 86, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
120 4 0.05
121 78 0.91
122 4 0.05
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (121 bp):
TTCCTAAAGATGGCATGACATCTTCATCACGTAGGAACCGTGTCATCCCCTGACCAAACCTCCTC
ATCACGTAGCAGTCGTGTCATCCCTAGACAACCAGTCGTCCTCCGAGTTATCACTC
Found at i:152900 original size:43 final size:40
Alignment explanation
Indices: 152787--152900 Score: 104
Period size: 40 Copynumber: 2.8 Consensus size: 40
152777 CTAAAGATGG
* * *
152787 CCAGACCTCTTTATCACGTATGAGCCGTGTCATCCACCGA
1 CCAGACCTCTTTATCACGTATGAGCAGTGTCACCCAACGA
* * * * * *
152827 CCATATCTCCTCATCGCGTA-GCAGCTGTGTCACCCTTAGACGA
1 CCAGACCTCTTTATCACGTATG-AGCAGTGTCACCC--A-ACGA
152870 CCAGACCTCTTTATCACGTATGAGCAGTGTC
1 CCAGACCTCTTTATCACGTATGAGCAGTGTC
152901 GTCTTCCCCC
Statistics
Matches: 55, Mismatches: 14, Indels: 7
0.72 0.18 0.09
Matches are distributed among these distances:
39 1 0.02
40 26 0.47
42 1 0.02
43 26 0.47
44 1 0.02
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.26
Consensus pattern (40 bp):
CCAGACCTCTTTATCACGTATGAGCAGTGTCACCCAACGA
Found at i:159779 original size:29 final size:29
Alignment explanation
Indices: 159737--159819 Score: 130
Period size: 29 Copynumber: 2.9 Consensus size: 29
159727 AACCCAACCA
*
159737 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACGCCCAGCGACCTCC
*
159766 TAGGTCGCCATGCACGCCCGGCGACCTCC
1 TAGGTCGCCATGCACGCCCAGCGACCTCC
* *
159795 TAGGTCGCCATGCATGCCCGGCGAC
1 TAGGTCGCCATGCACGCCCAGCGAC
159820 ATCCCCTGCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.16, C:0.42, G:0.27, T:0.16
Consensus pattern (29 bp):
TAGGTCGCCATGCACGCCCAGCGACCTCC
Found at i:160036 original size:27 final size:27
Alignment explanation
Indices: 159998--160049 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
159988 ATCAACGGCT
159998 CGTGATTCTTCAATTATTGGTGCATGG
1 CGTGATTCTTCAATTATTGGTGCATGG
160025 CGTGATTCTTCAATTATTGGTGCAT
1 CGTGATTCTTCAATTATTGGTGCAT
160050 AGAAGCCGAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.19, C:0.15, G:0.23, T:0.42
Consensus pattern (27 bp):
CGTGATTCTTCAATTATTGGTGCATGG
Found at i:162467 original size:26 final size:24
Alignment explanation
Indices: 162407--162467 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
162397 TACTAATATT
*
162407 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
162431 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
162458 ATTTAATAAT
1 A-TTAATAAT
162468 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:162855 original size:14 final size:14
Alignment explanation
Indices: 162836--162862 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
162826 CACATACACA
162836 ACAACAAAAAATAG
1 ACAACAAAAAATAG
162850 ACAACAAAAAATA
1 ACAACAAAAAATA
162863 ATAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:162855 original size:17 final size:17
Alignment explanation
Indices: 162833--162865 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
162823 TTACACATAC
162833 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
162850 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
162866 AATTACTCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:163226 original size:43 final size:48
Alignment explanation
Indices: 163179--163281 Score: 135
Period size: 49 Copynumber: 2.2 Consensus size: 48
163169 GTTTAAAGAC
*
163179 ACTAACAAATTAATTAA-T-ATTTTTTTTATAT-T-TA-ATAACTTAA
1 ACTAACAAACTAATTAACTAATTTTTTTTATATATATATATAACTTAA
**
163222 ACTAATTAACTAATTAACTAATTTTTTTTATATATAATATATAACTTAA
1 ACTAACAAACTAATTAACTAATTTTTTTTATATAT-ATATATAACTTAA
163271 ACTAACAAACT
1 ACTAACAAACT
163282 GATAATTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
43 14 0.29
44 1 0.02
45 13 0.27
46 1 0.02
48 2 0.04
49 18 0.37
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.45
Consensus pattern (48 bp):
ACTAACAAACTAATTAACTAATTTTTTTTATATATATATATAACTTAA
Found at i:163249 original size:47 final size:49
Alignment explanation
Indices: 163181--163275 Score: 131
Period size: 47 Copynumber: 2.0 Consensus size: 49
163171 TTAAAGACAC
* * *
163181 TAACAAATTAATTAATATTTTTTTTATAT-TTA-ATAACTTAAACTAAT
1 TAACAAATTAACTAATATTTTTTATATATAATATATAACTTAAACTAAT
* *
163228 TAACTAATTAACTAATTTTTTTTATATATAATATATAACTTAAACTAA
1 TAACAAATTAACTAATATTTTTTATATATAATATATAACTTAAACTAA
163276 CAAACTGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
47 25 0.61
48 2 0.05
49 14 0.34
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.47
Consensus pattern (49 bp):
TAACAAATTAACTAATATTTTTTATATATAATATATAACTTAAACTAAT
Found at i:163295 original size:21 final size:21
Alignment explanation
Indices: 163262--163302 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
163252 TATATAATAT
163262 ATAACTTAAACTAACAAACTG
1 ATAACTTAAACTAACAAACTG
* *
163283 ATAATTTATACTAACAAACT
1 ATAACTTAAACTAACAAACT
163303 AATTAACTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.17, G:0.02, T:0.29
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTG
Found at i:163601 original size:21 final size:23
Alignment explanation
Indices: 163567--163616 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 23
163557 AAATTTGACT
*
163567 ATTGAATAAAATAA-TATT-AGG
1 ATTGAATAAAATAACTATTGAGC
* *
163588 ATTGAATCATATAACTATTGAGC
1 ATTGAATAAAATAACTATTGAGC
163611 ATTGAA
1 ATTGAA
163617 AGTCTTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.50
22 4 0.17
23 8 0.33
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (23 bp):
ATTGAATAAAATAACTATTGAGC
Found at i:163854 original size:28 final size:29
Alignment explanation
Indices: 163814--163889 Score: 127
Period size: 28 Copynumber: 2.7 Consensus size: 29
163804 ATGATGATGC
163814 AGACCTACCATGTCGCCGGGACTCC-TCG
1 AGACCTACCATGTCGCCGGGACTCCATCG
* *
163842 AGACCTACCATGTCGTCGGGACTCCATGG
1 AGACCTACCATGTCGCCGGGACTCCATCG
163871 AGACCTACCATGTCGCCGG
1 AGACCTACCATGTCGCCGG
163890 CCATGGCAAC
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 24 0.55
29 20 0.45
ACGTcount: A:0.20, C:0.36, G:0.26, T:0.18
Consensus pattern (29 bp):
AGACCTACCATGTCGCCGGGACTCCATCG
Found at i:165849 original size:13 final size:13
Alignment explanation
Indices: 165831--165863 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
165821 AGCATTGTGA
*
165831 AAAGAAAATAATG
1 AAAGAAAATAAAG
165844 AAAGAAAATAAAG
1 AAAGAAAATAAAG
165857 AAAGAAA
1 AAAGAAA
165864 GACGGAGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
AAAGAAAATAAAG
Found at i:169670 original size:23 final size:23
Alignment explanation
Indices: 169644--169701 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
169634 AGAGTTTTAC
* *
169644 AGAGAATTTTACCGTGAAATTAG
1 AGAGAATTTTACCGTGAAACTAA
* * *
169667 AGAGAACTTTACGGTGAGACTAA
1 AGAGAATTTTACCGTGAAACTAA
169690 AGAGAATTTTAC
1 AGAGAATTTTAC
169702 TGTGGAAGGG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (23 bp):
AGAGAATTTTACCGTGAAACTAA
Found at i:169836 original size:12 final size:13
Alignment explanation
Indices: 169821--169853 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
169811 AGATGATTTT
169821 TTTTTAAAATA-A
1 TTTTTAAAATATA
169833 TTTTTAAAATATA
1 TTTTTAAAATATA
*
169846 ATTTTAAA
1 TTTTTAAA
169854 GGATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTTAAAATATA
Found at i:169976 original size:42 final size:43
Alignment explanation
Indices: 169894--169975 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
169884 TTAAAATTTA
* *
169894 TAATTTAATCATTAGTTTCAAAATCTAAACTTTTATTTTTATT
1 TAATTTAATCATTAATTTCAAAATATAAACTTTTATTTTTATT
* *
169937 TAATTTAGTCA-TAATTTCAATAATATAAATTTTTATTTT
1 TAATTTAATCATTAATTTCAA-AATATAAACTTTTATTTT
169976 ACATTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 8 0.24
43 26 0.76
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (43 bp):
TAATTTAATCATTAATTTCAAAATATAAACTTTTATTTTTATT
Found at i:169983 original size:13 final size:13
Alignment explanation
Indices: 169965--169989 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
169955 AATAATATAA
169965 ATTTTTATTTTAC
1 ATTTTTATTTTAC
169978 ATTTTTATTTTA
1 ATTTTTATTTTA
169990 ATTATATTTA
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:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTTTATTTTAC
Found at i:173799 original size:20 final size:19
Alignment explanation
Indices: 173745--173848 Score: 74
Period size: 21 Copynumber: 5.4 Consensus size: 19
173735 TAATATTATC
*
173745 TAAAATTAAATAGATAATTT
1 TAAAA-TAAATAAATAATTT
* *
173765 AAAAAT-AAT--ATTA-TT
1 TAAAATAAATAAATAATTT
173780 TAAAATAAATAAATAATATTT
1 TAAAATAAATAAAT-A-ATTT
* *
173801 TCAAATAAATAATATGATTT
1 TAAAATAAATAA-ATAATTT
173821 TAAAAAGTAAATAAAT-ATTT
1 T-AAAA-TAAATAAATAATTT
173841 TAAAATAA
1 TAAAATAA
173849 TTTCATAATA
Statistics
Matches: 68, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
15 7 0.10
16 6 0.09
18 8 0.12
19 5 0.07
20 15 0.22
21 18 0.26
22 9 0.13
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.38
Consensus pattern (19 bp):
TAAAATAAATAAATAATTT
Found at i:173806 original size:21 final size:21
Alignment explanation
Indices: 173767--173848 Score: 82
Period size: 21 Copynumber: 3.9 Consensus size: 21
173757 GATAATTTAA
173767 AAATAATATTATTTAAAATAAAT
1 AAATAATA-T-TTTAAAATAAAT
*
173790 AAATAATATTTTCAAATAAAT
1 AAATAATATTTTAAAATAAAT
*
173811 -AAT-ATGATTTT-AAA-AAGT
1 AAATAAT-ATTTTAAAATAAAT
173829 AAATAAATATTTTAAAATAA
1 AAAT-AATATTTTAAAATAA
173849 TTTCATAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
18 3 0.06
19 8 0.16
20 13 0.25
21 16 0.31
22 3 0.06
23 8 0.16
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (21 bp):
AAATAATATTTTAAAATAAAT
Found at i:173812 original size:40 final size:40
Alignment explanation
Indices: 173767--173848 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
173757 GATAATTTAA
* *
173767 AAATAATATTATTTAAAATAAATAAAT-AATATTTTCAAAT
1 AAATAATATGATTTAAAA-AAATAAATAAATATTTTAAAAT
* *
173807 AAATAATATGATTTTAAAAAGTAAATAAATATTTTAAAAT
1 AAATAATATGATTTAAAAAAATAAATAAATATTTTAAAAT
173847 AA
1 AA
173849 TTTCATAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 7 0.19
40 30 0.81
ACGTcount: A:0.59, C:0.01, G:0.02, T:0.38
Consensus pattern (40 bp):
AAATAATATGATTTAAAAAAATAAATAAATATTTTAAAAT
Found at i:175435 original size:23 final size:24
Alignment explanation
Indices: 175400--175449 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
175390 ATTTATAAAG
*
175400 TTATATTAAATTATTTTAAAATTT
1 TTATATTAAATTATTATAAAATTT
* *
175424 TTAT-TTATATTATTATGAAATTT
1 TTATATTAAATTATTATAAAATTT
175447 TTA
1 TTA
175450 AAAAGTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTATATTAAATTATTATAAAATTT
Found at i:175498 original size:23 final size:23
Alignment explanation
Indices: 175457--175523 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
175447 TTAAAAAGTT
* *
175457 TTATTTAGTTT-TTTCAAATCACA
1 TTATTTA-TTTATTTGAAATAACA
*
175480 TTATTTATTTATTTGAAATAATA
1 TTATTTATTTATTTGAAATAACA
* *
175503 TGAATTATTTATTTGAAATAA
1 TTATTTATTTATTTGAAATAA
175524 TATATTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
22 3 0.08
23 35 0.92
ACGTcount: A:0.37, C:0.04, G:0.06, T:0.52
Consensus pattern (23 bp):
TTATTTATTTATTTGAAATAACA
Found at i:175736 original size:24 final size:23
Alignment explanation
Indices: 175700--175755 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
175690 TAAATAAATA
175700 TTTTTATAATATTAT-AAATATTC
1 TTTTTATAATATT-TCAAATATTC
* *
175723 TTTTTATAATTATTTCATATATTG
1 TTTTTATAA-TATTTCAAATATTC
175747 TTTTTATAA
1 TTTTTATAA
175756 AAATATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 10 0.34
24 19 0.66
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTTATAATATTTCAAATATTC
Found at i:176418 original size:2 final size:2
Alignment explanation
Indices: 176411--176467 Score: 84
Period size: 2 Copynumber: 29.5 Consensus size: 2
176401 AGAATTTTCC
176411 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T CAT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
176453 AT AT -T A- AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
176468 CATTATATTT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
1 3 0.06
2 47 0.92
3 1 0.02
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:176472 original size:14 final size:15
Alignment explanation
Indices: 176411--176475 Score: 96
Period size: 16 Copynumber: 4.3 Consensus size: 15
176401 AGAATTTTCC
176411 ATATATATATATATAT
1 ATATATATATATAT-T
176427 ATATATATATATATT
1 ATATATATATATATT
176442 CATATATATATATATT
1 -ATATATATATATATT
*
176458 A-ATATATATACATT
1 ATATATATATATATT
176472 ATAT
1 ATAT
176476 TTAGAGGTGG
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
14 13 0.28
15 4 0.09
16 29 0.63
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (15 bp):
ATATATATATATATT
Found at i:176776 original size:21 final size:20
Alignment explanation
Indices: 176731--176778 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
176721 ATTTCATTTC
*
176731 AGGTCAGCCTTTATATTTTT
1 AGGTCAACCTTTATATTTTT
*
176751 GGGTCAACCTTTATATTTTTT
1 AGGTCAACCTTTATA-TTTTT
176772 AGGTCAA
1 AGGTCAA
176779 TTGTTGTCGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.23, C:0.15, G:0.17, T:0.46
Consensus pattern (20 bp):
AGGTCAACCTTTATATTTTT
Found at i:182798 original size:20 final size:20
Alignment explanation
Indices: 182768--182827 Score: 84
Period size: 23 Copynumber: 2.8 Consensus size: 20
182758 AACCATTGGG
182768 GCCTGATGGTATCGATACTAT
1 GCCT-ATGGTATCGATACTAT
182789 GCCTATGGTATCGATGATACTAT
1 GCCTATGGTATC---GATACTAT
182812 GCCTATGGTATCGATA
1 GCCTATGGTATCGATA
182828 ATACTATGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
20 12 0.33
21 4 0.11
23 20 0.56
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.33
Consensus pattern (20 bp):
GCCTATGGTATCGATACTAT
Found at i:182811 original size:23 final size:23
Alignment explanation
Indices: 182781--182836 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
182771 TGATGGTATC
182781 GATACTATGCCTATGGTATCGAT
1 GATACTATGCCTATGGTATCGAT
182804 GATACTATGCCTATGGTATCGAT
1 GATACTATGCCTATGGTATCGAT
*
182827 AATACTATGC
1 GATACTATGC
182837 AAAGTAGTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (23 bp):
GATACTATGCCTATGGTATCGAT
Found at i:184058 original size:175 final size:176
Alignment explanation
Indices: 183778--184144 Score: 612
Period size: 175 Copynumber: 2.1 Consensus size: 176
183768 AAATTAAATG
* *
183778 TTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAATTATAAAATAAAAATTTC
1 TTTTTTAATTTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTC
183843 AGATAAATTTTTTAATTAATTAACATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
66 AGATAAATTTTTTAATTAATTAACATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
*
183908 TTGAGTTTTAAATGGTTTGGGATTAGCCCATATGTTATATATAATA
131 TTGAGTTTTAAATGGTTTGGGATGAGCCCATATGTTATATATAATA
183954 TTTTTTAATTTAAAAAAACAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTT
1 TTTTTTAATTTAAAAAAA-AGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTT
* * *
184019 TATAT-AA-TTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTA
65 CAGATAAATTTTTTAATTAATTAACATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTA
* *
184082 ATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTATATATAATA
130 ATTGAGTTTTAAATGGTTTGGGATGAGCCCATATGTTATATATAATA
* *
184129 TATTTAATATTTAAAA
1 TTTTTTA-ATTTAAAA
184145 TTTAATTTCG
Statistics
Matches: 179, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
175 104 0.58
176 27 0.15
177 48 0.27
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.45
Consensus pattern (176 bp):
TTTTTTAATTTAAAAAAAAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAATTTC
AGATAAATTTTTTAATTAATTAACATTGATTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAA
TTGAGTTTTAAATGGTTTGGGATGAGCCCATATGTTATATATAATA
Found at i:191332 original size:21 final size:21
Alignment explanation
Indices: 191294--191341 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
191284 GCTATTTTTA
*
191294 TATTTGTATTATATTATA-TT
1 TATTTGTATTATAGTATACTT
191314 TATTTGTATATATAGTATACTT
1 TATTTGTAT-TATAGTATACTT
*
191336 TTTTTG
1 TATTTG
191342 GTTGAATACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.38
21 8 0.33
22 7 0.29
ACGTcount: A:0.27, C:0.02, G:0.08, T:0.62
Consensus pattern (21 bp):
TATTTGTATTATAGTATACTT
Found at i:197142 original size:2 final size:2
Alignment explanation
Indices: 197135--197173 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
197125 TTCTTCTGTT
*
197135 AC AC AC AC AC AC AC AC AC AC AC AC CC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
197174 TTAAAGCCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.51, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:201019 original size:21 final size:21
Alignment explanation
Indices: 200984--201132 Score: 257
Period size: 21 Copynumber: 7.2 Consensus size: 21
200974 TACATATTCG
200984 CGTTGCGATAG--TCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
201003 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
* *
201024 CGTTGGGATAGTCTCCAAATT
1 CGTTGCGATAGTCTCCAAGTT
*
201045 CGTTGCGATAGTCTCCAAATT
1 CGTTGCGATAGTCTCCAAGTT
201066 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
201087 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
201108 CGTTGCGATAGTCTCCAAGTT
1 CGTTGCGATAGTCTCCAAGTT
201129 CGTT
1 CGTT
201133 ATTGCATTTA
Statistics
Matches: 124, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
19 11 0.09
21 113 0.91
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCTCCAAGTT
Found at i:201838 original size:21 final size:21
Alignment explanation
Indices: 201812--202187 Score: 626
Period size: 21 Copynumber: 17.9 Consensus size: 21
201802 TGCGATTTTG
*
201812 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
201833 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
201854 GACTATCGCAACGCACTTGGA
1 GACTATCGCAACGAACTTGGA
201875 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
201896 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
201917 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
201938 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
* *
201959 GACTATCGCAATGAATTTGGA
1 GACTATCGCAACGAACTTGGA
*
201980 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
202001 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
202022 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
202043 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
202064 GACTATCACAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
202085 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
*
202106 GACTATCGCAACGAATTTGGA
1 GACTATCGCAACGAACTTGGA
202127 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
** * *
202148 GACTATCATAATGCACTTGGA
1 GACTATCGCAACGAACTTGGA
202169 GACTATCGCAACGAACTTG
1 GACTATCGCAACGAACTTG
202188 AAAAATCGCA
Statistics
Matches: 332, Mismatches: 23, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 332 1.00
ACGTcount: A:0.33, C:0.22, G:0.23, T:0.22
Consensus pattern (21 bp):
GACTATCGCAACGAACTTGGA
Found at i:202204 original size:21 final size:21
Alignment explanation
Indices: 202173--202221 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
202163 CTTGGAGACT
202173 ATCGCAA--CGAACTT-GAAAA
1 ATCGCAACGCGAACTTAG-AAA
202192 ATCGCAACGCGAACTTAGAAA
1 ATCGCAACGCGAACTTAGAAA
202213 ATCGCAACG
1 ATCGCAACG
202222 TTAACTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.26
21 19 0.70
22 1 0.04
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.14
Consensus pattern (21 bp):
ATCGCAACGCGAACTTAGAAA
Found at i:205702 original size:87 final size:87
Alignment explanation
Indices: 205546--205711 Score: 237
Period size: 87 Copynumber: 1.9 Consensus size: 87
205536 TCGTGATTCC
* * *
205546 CCTCCAGCAATTGATCCTTAAAAGCAGACGAATCAGGAAGCTTTTTCTCAAAACTGTTTCCCTCT
1 CCTCCAGCAATTGATCCTCAAAAGCAGACGAATCAGGAAGCTTTTTCTCAAAACTATTCCCCTCT
*
205611 TCATAGACGACAATTTGACCCT
66 TCATAGACAACAATTTGACCCT
* * *
205633 CCTCTAGCAGTTGATCCTCAAAAG-ATGATGAATCAGGAAGCTTTTTCTCAAAACTATTACCCCT
1 CCTCCAGCAATTGATCCTCAAAAGCA-GACGAATCAGGAAGCTTTTTCTCAAAACTATT-CCCCT
205697 -TTCATAGACAACAAT
64 CTTCATAGACAACAAT
205712 ATCACCAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
86 1 0.01
87 65 0.93
88 4 0.06
ACGTcount: A:0.32, C:0.26, G:0.13, T:0.29
Consensus pattern (87 bp):
CCTCCAGCAATTGATCCTCAAAAGCAGACGAATCAGGAAGCTTTTTCTCAAAACTATTCCCCTCT
TCATAGACAACAATTTGACCCT
Found at i:206063 original size:171 final size:171
Alignment explanation
Indices: 205773--206119 Score: 532
Period size: 171 Copynumber: 2.0 Consensus size: 171
205763 AGTTACTTTG
* * * *
205773 ACAGAGTTCCTATCAAATTCATTTGGAAAAGCTTCACAAGAAGGTTTGCTGCTTTTTTTAATCAT
1 ACAGAGTTCCGATCAAATTCATTTGGAAAAGCTTCACAAGAAGGCTTGATGCTGTTTTTAATCAT
* *
205838 ATTTCCGGCATCATCCTCCACATCGTTGCAGGAATAAACTTTATATGCACCTTGCTTTTCCATTT
66 ATTTCCGGCATCATCCTCCACATCGTTGCAGGAATAAACTTCATATGAACCTTGCTTTTCCATTT
* * * * *
205903 TTTCAGTAGCTGGCTCTTCAGGTTTAGAATGAATACCTTCT
131 TTTCAGAAGATGGCTCCTCACGTCTAGAATGAATACCTTCT
* *
205944 ACAGAGTTCCGATCAAATTCATTTGGAATAGCTTCACAAGAAGGCTTGATGCTGTTTTTACTCAT
1 ACAGAGTTCCGATCAAATTCATTTGGAAAAGCTTCACAAGAAGGCTTGATGCTGTTTTTAATCAT
* * * *
206009 ATTTCCGGCATCCTCCTCCATATTGTTGCAGGAATAAGCTTCATATGAACCTTGCTTTTCCATTT
66 ATTTCCGGCATCATCCTCCACATCGTTGCAGGAATAAACTTCATATGAACCTTGCTTTTCCATTT
*
206074 TTTCAGAAGATGGTTCCTCACGTCTAGAATGAATACCTTCT
131 TTTCAGAAGATGGCTCCTCACGTCTAGAATGAATACCTTCT
206115 ACAGA
1 ACAGA
206120 TAGCCTAGGA
Statistics
Matches: 158, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
171 158 1.00
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (171 bp):
ACAGAGTTCCGATCAAATTCATTTGGAAAAGCTTCACAAGAAGGCTTGATGCTGTTTTTAATCAT
ATTTCCGGCATCATCCTCCACATCGTTGCAGGAATAAACTTCATATGAACCTTGCTTTTCCATTT
TTTCAGAAGATGGCTCCTCACGTCTAGAATGAATACCTTCT
Found at i:209134 original size:20 final size:20
Alignment explanation
Indices: 209098--209135 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
209088 AAATATAAAA
*
209098 ATTAAACTATATTTATACTT
1 ATTAAACTATATATATACTT
209118 ATTAATACTAT-TATATAC
1 ATTAA-ACTATATATATAC
209136 AAAATTTATC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.11, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTAAACTATATATATACTT
Found at i:209333 original size:36 final size:35
Alignment explanation
Indices: 209220--209335 Score: 103
Period size: 36 Copynumber: 3.3 Consensus size: 35
209210 TTATTGAGAA
*
209220 AAAATATATTATCAATATTTTTAACATGTGGGTAT
1 AAAATATATTATCAATATTTTTAACATGTGGATAT
* * ****
209255 AAAAT-TATTATGAAATAATAATTTAA-ATACAAATA-
1 AAAATATATTAT-CAAT-AT-TTTTAACATGTGGATAT
209290 ACAAATATATTATCAATACTTTTTAACATGTGGATAT
1 A-AAATATATTATCAATA-TTTTTAACATGTGGATAT
209327 AAAATATAT
1 AAAATATAT
209336 CAATTTAAAC
Statistics
Matches: 60, Mismatches: 13, Indels: 15
0.68 0.15 0.17
Matches are distributed among these distances:
34 6 0.10
35 15 0.25
36 27 0.45
37 12 0.20
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (35 bp):
AAAATATATTATCAATATTTTTAACATGTGGATAT
Found at i:209380 original size:17 final size:18
Alignment explanation
Indices: 209360--209396 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
209350 ATAAAATATA
209360 AAAAATATA-ATTATAAT
1 AAAAATATATATTATAAT
*
209377 AAAAATATATTTTATAAT
1 AAAAATATATATTATAAT
209395 AA
1 AA
209397 CTCACTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
AAAAATATATATTATAAT
Found at i:210486 original size:2 final size:2
Alignment explanation
Indices: 210443--210472 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
210433 GTAATTGTAA
210443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
210473 TCATGAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:213864 original size:14 final size:14
Alignment explanation
Indices: 213845--213872 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
213835 TCTTAACAAT
213845 CCATCAATTTCTTA
1 CCATCAATTTCTTA
213859 CCATCAATTTCTTA
1 CCATCAATTTCTTA
213873 TATTAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.43
Consensus pattern (14 bp):
CCATCAATTTCTTA
Found at i:219098 original size:23 final size:21
Alignment explanation
Indices: 219049--219101 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
219039 TGAATTGCTC
* *
219049 AAGAAAATA-AGAAAGGATTT
1 AAGAAAATAGAGAAAAGATTG
219069 AAG-AAATAGAGAAGATAGATTG
1 AAGAAAATAGAGAA-A-AGATTG
219091 AAGAAAATAGA
1 AAGAAAATAGA
219102 ATCATAACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 5 0.19
20 7 0.26
21 1 0.04
22 7 0.26
23 7 0.26
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (21 bp):
AAGAAAATAGAGAAAAGATTG
Found at i:222484 original size:3 final size:3
Alignment explanation
Indices: 222476--222504 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
222466 GGCTTCTCAT
222476 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
222505 TACCCCATCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:226682 original size:19 final size:18
Alignment explanation
Indices: 226658--226693 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
226648 TATATATATA
226658 TATATATATTAATCTTAAT
1 TATATATATTAAT-TTAAT
*
226677 TATATATTTTAATTTAA
1 TATATATATTAATTTAA
226694 GTATGAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TATATATATTAATTTAAT
Found at i:226683 original size:2 final size:2
Alignment explanation
Indices: 226639--226666 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
226629 AATTAAAATC
226639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
226667 TAATCTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228829 original size:6 final size:6
Alignment explanation
Indices: 228818--228876 Score: 118
Period size: 6 Copynumber: 9.8 Consensus size: 6
228808 GTATAACATC
228818 TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA
1 TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA TCTAAA
228866 TCTAAA TCTAA
1 TCTAAA TCTAA
228877 CTCTTACATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (6 bp):
TCTAAA
Found at i:234784 original size:57 final size:57
Alignment explanation
Indices: 234692--234803 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 57
234682 GGCAATTCTT
*
234692 GATTTTCTCGCGAAATTAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCAGTC
1 GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCAGTC
*
234749 GATTTTCTCGCGAAATCAGTTTGGTGTATCGAACCAGACTGACGTTCTGCTGCAG
1 GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCAG
234804 CCGTGAATTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.32
Consensus pattern (57 bp):
GATTTTCTCGCGAAATCAGTTTGGTGTATCCAACCAGACTGACGTTCTGCTGCAGTC
Found at i:238374 original size:30 final size:30
Alignment explanation
Indices: 238338--238410 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
238328 GCTTAATTCT
*
238338 CATTTTGGTCACTTATGTTATCGATTGTTA
1 CATTTTGGTCACTTATGTTATCGACTGTTA
*
238368 CATTTTGGTTACTTATGTTATCGACTGTTA
1 CATTTTGGTCACTTATGTTATCGACTGTTA
238398 CATTTTGGTCACT
1 CATTTTGGTCACT
238411 AAGTCGTTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.49
Consensus pattern (30 bp):
CATTTTGGTCACTTATGTTATCGACTGTTA
Found at i:241237 original size:13 final size:13
Alignment explanation
Indices: 241219--241245 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
241209 TTACAGACGC
241219 GCATATGAAGACT
1 GCATATGAAGACT
241232 GCATATGAAGACT
1 GCATATGAAGACT
241245 G
1 G
241246 TTCAACTATG
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:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GCATATGAAGACT
Found at i:241851 original size:30 final size:31
Alignment explanation
Indices: 241820--241879 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
241810 TTAATTGAAA
* *
241820 TTAGAGATCAAAATGATATTTTATCTAAAAT
1 TTAGAGATCAAAATGATACTTCATCTAAAAT
* * *
241851 TTAGGGGTCAAATTGATACTTCATCTAAA
1 TTAGAGATCAAAATGATACTTCATCTAAA
241880 GTTTGAAGTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (31 bp):
TTAGAGATCAAAATGATACTTCATCTAAAAT
Found at i:254667 original size:19 final size:20
Alignment explanation
Indices: 254640--254681 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
254630 CGAATAATTG
* *
254640 AATCGAATATAATAT-TTAA
1 AATCAAATATAAAATCTTAA
254659 AATCAAATATAAAATCTTAA
1 AATCAAATATAAAATCTTAA
254679 AAT
1 AAT
254682 TAATTTACAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (20 bp):
AATCAAATATAAAATCTTAA
Found at i:256343 original size:13 final size:13
Alignment explanation
Indices: 256325--256378 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
256315 GTCATAAATC
256325 TATGACGCGCATT
1 TATGACGCGCATT
* *
256338 TATGACACTCA-T
1 TATGACGCGCATT
**
256350 TATGACGCATATT
1 TATGACGCGCATT
256363 TATGACGCGCATT
1 TATGACGCGCATT
256376 TAT
1 TAT
256379 ATGCTCATTG
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
12 9 0.27
13 24 0.73
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:256375 original size:25 final size:25
Alignment explanation
Indices: 256325--256375 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
256315 GTCATAAATC
* *
256325 TATGACGCGCATTTATGACACTCAT
1 TATGACGCACATTTATGACACGCAT
* *
256350 TATGACGCATATTTATGACGCGCAT
1 TATGACGCACATTTATGACACGCAT
256375 T
1 T
256376 TATATGCTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (25 bp):
TATGACGCACATTTATGACACGCAT
Found at i:262917 original size:6 final size:6
Alignment explanation
Indices: 262892--263203 Score: 522
Period size: 6 Copynumber: 52.3 Consensus size: 6
262882 ATAGAAAGAG
* ** * *
262892 GAGGAA GAGGAG GAAAAA GAAGAA GAAGAA GAGGAA GAGGAA GAGGAA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
262940 GAGGAA GAGGAA GAGGAA GAGGAA GAGG-A GAGGAA GAGGAA GAGGGAA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GA-GGAA
262988 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
263036 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
263084 GA--AA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
263130 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
1 GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA GAGGAA
* * *
263178 GAAGAT GAAGAA GAGGAA GAGGAA GA
1 GAGGAA GAGGAA GAGGAA GAGGAA GA
263204 TGAAATGAAA
Statistics
Matches: 292, Mismatches: 10, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
4 4 0.01
5 5 0.02
6 277 0.95
7 6 0.02
ACGTcount: A:0.51, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GAGGAA
Done.