Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007515.1 Hibiscus syriacus cultivar Beakdansim tig00020905_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: 104589
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1767 original size:23 final size:22
Alignment explanation
Indices: 1709--1770 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 22
1699 ATAAAAGAAT
1709 AATATAGTATTTTTATTTAAAATA
1 AATATA-TA-TTTTATTTAAAATA
* * * *
1733 AATTTTTTTTTTATTTTAAATAA
1 AATATATATTTTATTTAAAAT-A
1756 AATATATATTTTATT
1 AATATATATTTTATT
1771 CTTTTATCTT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
22 12 0.40
23 14 0.47
24 4 0.13
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
AATATATATTTTATTTAAAATA
Found at i:1821 original size:19 final size:21
Alignment explanation
Indices: 1786--1833 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1776 ATCTTTTATT
*
1786 AATATATATTCATTTAA-TAA
1 AATATATAATCATTTAACTAA
1806 AATATATAAT-ATTTAAGCTAA
1 AATATATAATCATTTAA-CTAA
1827 AATATAT
1 AATATAT
1834 TATAACTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 6 0.24
20 9 0.36
21 10 0.40
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (21 bp):
AATATATAATCATTTAACTAA
Found at i:7944 original size:23 final size:23
Alignment explanation
Indices: 7914--7967 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
7904 ATGTTGAATT
* *
7914 ATTCAGCAGTGTTTTACTGTTTC
1 ATTCAGCAATATTTTACTGTTTC
7937 ATTCAGCAATATTTTACTGTTTC
1 ATTCAGCAATATTTTACTGTTTC
7960 ATTCAGCA
1 ATTCAGCA
7968 TGGTTTTCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (23 bp):
ATTCAGCAATATTTTACTGTTTC
Found at i:7974 original size:23 final size:23
Alignment explanation
Indices: 7914--7974 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
7904 ATGTTGAATT
7914 ATTCAGCA-GTGTTTTACTGTTTC
1 ATTCAGCATG-GTTTTACTGTTTC
*
7937 ATTCAGCAAT-ATTTTACTGTTTC
1 ATTCAGC-ATGGTTTTACTGTTTC
7960 ATTCAGCATGGTTTT
1 ATTCAGCATGGTTTT
7975 CATTCATAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 2 0.06
23 30 0.91
24 1 0.03
ACGTcount: A:0.21, C:0.16, G:0.15, T:0.48
Consensus pattern (23 bp):
ATTCAGCATGGTTTTACTGTTTC
Found at i:22091 original size:31 final size:31
Alignment explanation
Indices: 22053--22208 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
22043 CCCGAAGGAC
* * *
22053 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
22084 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
22115 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
22146 CAGTCCGTATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
22177 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
22208 C
1 C
22209 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:22410 original size:23 final size:24
Alignment explanation
Indices: 22384--22430 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
22374 ATATACCTGT
*
22384 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
22407 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
22431 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:23065 original size:21 final size:21
Alignment explanation
Indices: 23035--23079 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
23025 ATTCTGTCGT
* *
23035 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
23056 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
23077 TTG
1 TTG
23080 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:26157 original size:31 final size:31
Alignment explanation
Indices: 26119--26274 Score: 233
Period size: 31 Copynumber: 5.0 Consensus size: 31
26109 CCCGAAGGAC
* * *
26119 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
26150 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
26181 CAGTCCGTATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
26212 CAGTCCGTATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
26243 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
26274 C
1 C
26275 CCTCGACCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:26478 original size:23 final size:24
Alignment explanation
Indices: 26452--26498 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
26442 ATATACCTGT
*
26452 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
26475 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
26499 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:27130 original size:21 final size:21
Alignment explanation
Indices: 27100--27144 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
27090 ATTCTGTCGT
* *
27100 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
27121 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
27142 TTG
1 TTG
27145 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:27908 original size:17 final size:17
Alignment explanation
Indices: 27860--27910 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
27850 GAACGTGTCC
*
27860 ATTAT-ATTAAATATTT
1 ATTATAATTTAATATTT
*
27876 TTTATAATTTAA-ATTT
1 ATTATAATTTAATATTT
27892 ATT-TAATTTATATATTT
1 ATTATAATTTA-ATATTT
27909 AT
1 AT
27911 CTTTCAACCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 7 0.24
16 11 0.38
17 11 0.38
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTATAATTTAATATTT
Found at i:28053 original size:21 final size:21
Alignment explanation
Indices: 28020--28059 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
28010 TTTACCGTAC
*
28020 ACCCGAACTAAATTTGACCTG
1 ACCCGAACTAAATTAGACCTG
28041 ACCCGAA-TAAAATTAGACC
1 ACCCGAACT-AAATTAGACC
28060 AAATATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.40, C:0.28, G:0.12, T:0.20
Consensus pattern (21 bp):
ACCCGAACTAAATTAGACCTG
Found at i:28333 original size:17 final size:17
Alignment explanation
Indices: 28294--28335 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
28284 TATTAGATTA
*
28294 AATATTTTTTATAATTT
1 AATATTTATTATAATTT
28311 AA-ATTTATT-TAATTT
1 AATATTTATTATAATTT
28326 ATATATTTAT
1 A-ATATTTAT
28336 CTTCCAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 7 0.32
16 7 0.32
17 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATATTTATTATAATTT
Found at i:29086 original size:2 final size:2
Alignment explanation
Indices: 29079--29117 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
29069 TTTATTTATT
29079 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 T
29118 GGTTTGCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29221 original size:74 final size:72
Alignment explanation
Indices: 29143--29623 Score: 499
Period size: 74 Copynumber: 6.7 Consensus size: 72
29133 TTAAAATACA
*
29143 TATAATATATAGTTTTAAAAACGGTTTTTGGAAATATATATAACATATAGTTTTTAAAAACATTT
1 TATAATATATAGTTTTAAAAAC--TTTTTGGAAATATATATAATATATAGTTTTTAAAAACATTT
29208 TGAAAAACT
64 TGAAAAACT
* * *
29217 TATAATATATAGGTTTAAAAACATTTTTTGAAA-ATATATAATATATAATTTTT-AAAACATTTT
1 TATAATATATAGTTTTAAAAAC-TTTTTGGAAATATATATAATATATAGTTTTTAAAAACATTTT
29280 G-AAAACTT
65 GAAAAAC-T
* * * * *
29288 ATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTTTTTAAAACATTTT
1 -TATAATATATAGTTTTAAAAACTTTTTGGAAATATATATAATATATAGTTTTTAAAAACATTTT
29353 GAAAAACTT
65 GAAAAAC-T
* * * * *
29362 ATATAATATATAGTTTTGAAATCATTTTGAAAATATATATAATATATAGTTTTTTAAAACATTTT
1 -TATAATATATAGTTTTAAAAACTTTTTGGAAATATATATAATATATAGTTTTTAAAAACATTTT
29427 GAAAAACT
65 GAAAAACT
*
29435 TATATAGTATATAGTTTTAAAAACATTTTTTGAAA-ACTTATATAATATATAG-TTTTAAAAACA
1 TATA-A-TATATAGTTTTAAAAAC-TTTTTGGAAATA--TATATAATATATAGTTTTTAAAAACA
*
29498 TTTTGGAAAACT
61 TTTTGAAAAACT
* * * * *
29510 TAT-ATA-ATATTTTTTAAATCATTTT-GAAA-ACTATATAATATATAG-TTTTGAAAAC-TTTT
1 TATAATATATAGTTTTAAAAACTTTTTGGAAATA-TATATAATATATAGTTTTTAAAAACATTTT
**
29569 -AAAAAAA
65 GAAAAACT
* *
29576 TATAATTTATAG-TTTAAAAA-TATTTTTGAAATATATAT--TATATAGTTT
1 TATAATATATAGTTTTAAAAACT-TTTTGGAAATATATATAATATATAGTTT
29624 ATTTTATAAT
Statistics
Matches: 358, Mismatches: 33, Indels: 39
0.83 0.08 0.09
Matches are distributed among these distances:
66 14 0.04
67 18 0.05
68 35 0.10
69 6 0.02
70 9 0.03
71 30 0.08
72 62 0.17
73 23 0.06
74 116 0.32
75 31 0.09
76 14 0.04
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (72 bp):
TATAATATATAGTTTTAAAAACTTTTTGGAAATATATATAATATATAGTTTTTAAAAACATTTTG
AAAAACT
Found at i:29227 original size:36 final size:36
Alignment explanation
Indices: 29142--29623 Score: 482
Period size: 36 Copynumber: 13.4 Consensus size: 36
29132 TTTAAAATAC
* *
29142 ATATAATATATAGTTTTAAAAACGGTTTTTGGAAATA-T
1 ATATAATATATAGTTTTAAAAAC--ATTTT-GAAAAACT
*
29180 ATATAACATATAGTTTTTAAAAACATTTTGAAAAACT
1 ATATAATATATAG-TTTTAAAAACATTTTGAAAAACT
*
29217 -TATAATATATAGGTTTAAAAACATTTTTTG-AAAA-T
1 ATATAATATATAGTTTTAAAAACA--TTTTGAAAAACT
* *
29252 ATATAATATATAATTTTTAAAACATTTTG-AAAACTT
1 ATATAATATATAGTTTTAAAAACATTTTGAAAAAC-T
* *
29288 ATATAATATATAGTTTTGAAATCATTTTGAAAATA-T
1 ATATAATATATAGTTTTAAAAACATTTTGAAAA-ACT
*
29324 ATATAATATATAGTTTTTTAAAACATTTTGAAAAACTT
1 ATATAATATATAG-TTTTAAAAACATTTTGAAAAAC-T
* *
29362 ATATAATATATAGTTTTGAAATCATTTTGAAAATA-T
1 ATATAATATATAGTTTTAAAAACATTTTGAAAA-ACT
*
29398 ATATAATATATAGTTTTTTAAAACATTTTGAAAAACTT
1 ATATAATATATAG-TTTTAAAAACATTTTGAAAAAC-T
*
29436 ATATAGTATATAGTTTTAAAAACATTTTTTG-AAAACTT
1 ATATAATATATAGTTTTAAAAACA--TTTTGAAAAAC-T
*
29474 ATATAATATATAGTTTTAAAAACATTTTGGAAAACTT
1 ATATAATATATAGTTTTAAAAACATTTTGAAAAAC-T
*
29511 ATATAATAT-T--TTTT-AAATCATTTTG-AAAACT
1 ATATAATATATAGTTTTAAAAACATTTTGAAAAACT
* *
29542 ATATAATATATAGTTTTGAAAAC-TTTT-AAAAA-A
1 ATATAATATATAGTTTTAAAAACATTTTGAAAAACT
* *
29575 ATATAATTTATAG-TTTAAAAATATTTTTG--AAA-T
1 ATATAATATATAGTTTTAAAAACA-TTTTGAAAAACT
*
29608 ATATATTATATAGTTT
1 ATATAATATATAGTTT
29624 ATTTTATAAT
Statistics
Matches: 387, Mismatches: 29, Indels: 60
0.81 0.06 0.13
Matches are distributed among these distances:
31 10 0.03
32 13 0.03
33 36 0.09
34 31 0.08
35 15 0.04
36 103 0.27
37 93 0.24
38 71 0.18
39 15 0.04
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (36 bp):
ATATAATATATAGTTTTAAAAACATTTTGAAAAACT
Found at i:29612 original size:33 final size:32
Alignment explanation
Indices: 29435--29624 Score: 84
Period size: 33 Copynumber: 5.6 Consensus size: 32
29425 TTGAAAAACT
* *
29435 TATATAGTATATAGTTTTAAAAACATTTTTTGAAAA
1 TATATAATTTATAG-TTTAAAAA-A-TTTTTG-AAA
* *
29471 CTTATATAATATATAGTTTTAAAAACATTTTGGAAAA
1 --TATATAATTTATAG-TTTAAAAA-ATTTTTG-AAA
**
29508 CTTATATAATATT-T--TTTAAATCA-TTTTGAAAA
1 --TATATAAT-TTATAGTTTAAAAAATTTTTG-AAA
* * * **
29540 CTATATAATATATAGTTTTGAAAACTTTTAAAAA
1 -TATATAATTTATAG-TTTAAAAAATTTTTGAAA
*
29574 AATATAATTTATAGTTTAAAAATATTTTTGAAA
1 TATATAATTTATAGTTTAAAAA-ATTTTTGAAA
29607 TATAT-ATTATATAGTTTA
1 TATATAATT-TATAGTTTA
29625 TTTTATAATA
Statistics
Matches: 123, Mismatches: 21, Indels: 21
0.75 0.13 0.13
Matches are distributed among these distances:
30 1 0.01
31 9 0.07
32 18 0.15
33 33 0.27
34 14 0.11
35 3 0.02
37 20 0.16
38 25 0.20
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (32 bp):
TATATAATTTATAGTTTAAAAAATTTTTGAAA
Found at i:29689 original size:38 final size:40
Alignment explanation
Indices: 29620--29697 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
29610 ATATTATATA
* *
29620 GTTTATTTTATAATAGTATTATTTTTGTTATTATTTATTT
1 GTTTATTATATAATAATATTATTTTTGTTATTATTTATTT
* *
29660 GTTTATTATATATTAAT-TTATTTTT-TTATTTTTTATTT
1 GTTTATTATATAATAATATTATTTTTGTTATTATTTATTT
29698 TCTTTTTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 12 0.35
39 8 0.24
40 14 0.41
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (40 bp):
GTTTATTATATAATAATATTATTTTTGTTATTATTTATTT
Found at i:30784 original size:30 final size:27
Alignment explanation
Indices: 30750--30926 Score: 98
Period size: 29 Copynumber: 6.2 Consensus size: 27
30740 AGTTATTTTA
30750 TTTTTATTTATTTATTTCTCTTTTATATT
1 TTTTTATTTATTTATTT-TCTTTTATA-T
30779 GTTTTTATTTTATTTAACATTTTTCTTTTGATAT
1 -TTTTTA-TTTATTT---A-TTTTCTTTT-ATAT
*
30813 TTTTTA-TTATTATATTTTCCTTTTTTAT
1 TTTTTATTTATT-TATTTT-CTTTTATAT
*
30841 CCTTTTATTTATTTATTTAT-TTATT-TAT
1 -TTTTTATTTATTTATTT-TCTT-TTATAT
* *
30869 TTTTTCCTTTGATTTA--TTATTTTAT-T
1 TTTTT-ATTT-ATTTATTTTCTTTTATAT
* *
30895 TTATTATTTATTTATTTAT-ATTTATAT
1 TTTTTATTTATTTATTT-TCTTTTATAT
30922 TTTTT
1 TTTTT
30927 CCTTTTTTTG
Statistics
Matches: 119, Mismatches: 8, Indels: 43
0.70 0.05 0.25
Matches are distributed among these distances:
24 5 0.04
25 3 0.03
26 14 0.12
27 14 0.12
28 15 0.13
29 23 0.19
30 12 0.10
31 12 0.10
32 1 0.01
33 6 0.05
34 8 0.07
35 6 0.05
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.73
Consensus pattern (27 bp):
TTTTTATTTATTTATTTTCTTTTATAT
Found at i:30838 original size:36 final size:34
Alignment explanation
Indices: 30763--30829 Score: 89
Period size: 34 Copynumber: 1.9 Consensus size: 34
30753 TTATTTATTT
* *
30763 ATTTCTCTTTTATATTGTTTTTATTTTATTTAAC
1 ATTTTTCTTTTATATTGTTTTTATTATATTTAAC
*
30797 ATTTTTCTTTTGATATTTTTTATTATTATATTT
1 ATTTTTCTTTT-ATATTGTTT-TTATTATATTT
30830 TCCTTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 10 0.36
35 8 0.29
36 10 0.36
ACGTcount: A:0.21, C:0.06, G:0.03, T:0.70
Consensus pattern (34 bp):
ATTTTTCTTTTATATTGTTTTTATTATATTTAAC
Found at i:30852 original size:33 final size:31
Alignment explanation
Indices: 30815--30903 Score: 90
Period size: 33 Copynumber: 2.7 Consensus size: 31
30805 TTTGATATTT
*
30815 TTTATTATTATATTTTCCTT-TTTTATCCTTTTA
1 TTTATTATT-TATTTT--TTATTTTATCCTTTGA
*
30848 TTTATTTATTTATTTATTTATTTTTTCCTTTGA
1 TTTA-TTATTTATTT-TTTATTTTATCCTTTGA
30881 TTTATTATTTTATTTTATTATTT
1 TTTATTA-TTTATTTT-TTATTT
30904 ATTTATTTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
32 6 0.12
33 37 0.76
34 6 0.12
ACGTcount: A:0.19, C:0.07, G:0.01, T:0.73
Consensus pattern (31 bp):
TTTATTATTTATTTTTTATTTTATCCTTTGA
Found at i:30853 original size:4 final size:4
Alignment explanation
Indices: 30844--30984 Score: 82
Period size: 4 Copynumber: 35.0 Consensus size: 4
30834 TTTTTATCCT
*
30844 TTTA TTTA TTTA TTTA TTTA TTTA TTT- TTTCC TTTGA TTTA -TTA TTTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTT-A TTTA TTTA -TTTA
* * *
30893 TTT- TATTA TTTA TTTA TTTA --TA TTTA TATTT TTTCC TTTT TTTGA
1 TTTA T-TTA TTTA TTTA TTTA TTTA TTTA T-TTA TTT-A TTTA TTT-A
* * *
30938 TTTA -TTA TTTTA GTTTT TTTA GTT- TTTA TTTA TTTA -ATA TTTA TTTA
1 TTTA TTTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
30985 ATATTTTTTA
Statistics
Matches: 109, Mismatches: 13, Indels: 30
0.72 0.09 0.20
Matches are distributed among these distances:
2 2 0.02
3 14 0.13
4 68 0.62
5 25 0.23
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.73
Consensus pattern (4 bp):
TTTA
Found at i:30905 original size:57 final size:59
Alignment explanation
Indices: 30844--30983 Score: 170
Period size: 57 Copynumber: 2.5 Consensus size: 59
30834 TTTTTATCCT
30844 TTTATTTATTTATTTATTTATTTATTTTTTCC-TTTGATTTATTATTTTA-TTTTATTA
1 TTTATTTATTTATTTATTTATTTATTTTTTCCTTTTGATTTATTATTTTAGTTTTATTA
*
30901 TTTATTTATTTA--TATTTA--TATTTTTTCCTTTTTTTGATTTATTATTTTAGTTTTTTTA
1 TTTATTTATTTATTTATTTATTTATTTTTTCC---TTTTGATTTATTATTTTAGTTTTATTA
* *
30959 GTT-TTTATTTATTTA-ATATTTATTT
1 TTTATTTATTTATTTATTTATTTATTT
30984 AATATTTTTT
Statistics
Matches: 71, Mismatches: 3, Indels: 15
0.80 0.03 0.17
Matches are distributed among these distances:
53 10 0.14
55 6 0.08
57 37 0.52
58 11 0.15
59 2 0.03
60 5 0.07
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (59 bp):
TTTATTTATTTATTTATTTATTTATTTTTTCCTTTTGATTTATTATTTTAGTTTTATTA
Found at i:32099 original size:20 final size:20
Alignment explanation
Indices: 32074--32113 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
32064 TCAGATTGTC
*
32074 CAGGGGAACAGATTCTCCCT
1 CAGGGGAACAGATTCCCCCT
* *
32094 CAGGGGTACCGATTCCCCCT
1 CAGGGGAACAGATTCCCCCT
32114 GTCTAACGGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.35, G:0.25, T:0.20
Consensus pattern (20 bp):
CAGGGGAACAGATTCCCCCT
Found at i:32499 original size:34 final size:32
Alignment explanation
Indices: 32460--32529 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
32450 TTTTGTAAAG
* *
32460 GGGAAATGTTTTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAATGTTCTAGCTTAGCCCG-G-AAAAACTA
*
32494 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
32526 GGGA
1 GGGA
32530 GTTTGTAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (32 bp):
GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:38538 original size:21 final size:21
Alignment explanation
Indices: 38512--38804 Score: 164
Period size: 21 Copynumber: 14.0 Consensus size: 21
38502 GATTTACATA
38512 TTCGCATTGCGA-TAGTCCAAG
1 TTCGC-TTGCGATTAGTCCAAG
*
38533 TTCGCATTGCGA-TAGTCGAAG
1 TTCGC-TTGCGATTAGTCCAAG
* * *
38554 TTCACGTTGCGATTTATTCCAAA
1 TTCGC-TTGCGA-TTAGTCCAAG
* * *
38577 TTCG-TTGCGATTTATTTCAAA
1 TTCGCTTGCGA-TTAGTCCAAG
*
38598 TTCG-TTGTGA-TAGTCCAAG
1 TTCGCTTGCGATTAGTCCAAG
* *
38617 TTCGCGTCGCGATTTATTCCAAG
1 TTCGC-TTGCGA-TTAGTCCAAG
*
38640 TTCG-TTGCGA-TAGTCGAAG
1 TTCGCTTGCGATTAGTCCAAG
* * *
38659 TTCGTGTTGCGATTTATTCCAAA
1 TTCG-CTTGCGA-TTAGTCCAAG
* * *
38682 TTC-ATTGCGATTTATTCCAAA
1 TTCGCTTGCGA-TTAGTCCAAG
38703 TTCG-TTGCGA-TAGTCCAAG
1 TTCGCTTGCGATTAGTCCAAG
*
38722 TTCGCGTTGCGATTTATTCCAAG
1 TTCGC-TTGCGA-TTAGTCCAAG
**
38745 TTCG-TTGCGA-TAGTTGAAG
1 TTCGCTTGCGATTAGTCCAAG
* *
38764 TTCGCGTTGCGATTTATTCCAAA
1 TTCGC-TTGCGA-TTAGTCCAAG
38787 TTCG-TTGCGA-TAGTCCAA
1 TTCGCTTGCGATTAGTCCAA
38805 AATCGCAACG
Statistics
Matches: 220, Mismatches: 33, Indels: 40
0.75 0.11 0.14
Matches are distributed among these distances:
19 49 0.22
21 120 0.55
23 51 0.23
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (21 bp):
TTCGCTTGCGATTAGTCCAAG
Found at i:38604 original size:42 final size:42
Alignment explanation
Indices: 38558--38797 Score: 210
Period size: 42 Copynumber: 5.7 Consensus size: 42
38548 TCGAAGTTCA
* *
38558 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTTCAAATT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTT
* * * *
38600 CGTTGTGA--TAGTCCAAGTTCGCGTCGCGATTTATTCCAAGTT
1 CGTTGCGATTTATTCCAAATT--CGTTGCGATTTATTCCAAGTT
* * * *
38642 CGTTGCGA--TAGTCGAAGTTCGTGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATTC--GTTGCGATTTATTCCAAGTT
* *
38684 CATTGCGATTTATTCCAAATTCGTTGCGA--TAGTCCAAGTT
1 CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTT
* *
38724 CGCGTTGCGATTTATTCCAAGTTCGTTGCGA--TAGTT-GAAGTT
1 --CGTTGCGATTTATTCCAAATTCGTTGCGATTTA-TTCCAAGTT
38766 CGCGTTGCGATTTATTCCAAATTCGTTGCGAT
1 --CGTTGCGATTTATTCCAAATTCGTTGCGAT
38798 AGTCCAAAAT
Statistics
Matches: 167, Mismatches: 21, Indels: 19
0.81 0.10 0.09
Matches are distributed among these distances:
40 19 0.11
42 138 0.83
43 1 0.01
44 9 0.05
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (42 bp):
CGTTGCGATTTATTCCAAATTCGTTGCGATTTATTCCAAGTT
Found at i:38692 original size:63 final size:63
Alignment explanation
Indices: 38518--38755 Score: 227
Period size: 63 Copynumber: 3.8 Consensus size: 63
38508 CATATTCGCA
* * * *
38518 TTGCGATAGTCCAAGTTCGCATTGCGA--TAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCA--TTGCGATTTATTCCAAATTCG
* * * * * * * * *
38581 TTGCGATTTATTTCAAATT--CGTTGTGA--TAGTCCAAGTTCGCGTCGCGATTTATTCCAAGTT
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT--CATTGCGATTTATTCCAAATT
38642 CG
62 CG
* *
38644 TTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATTCATTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCATTGCGATTTATTCCAAATTCG
* *
38707 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGAT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCATTGCGAT
38756 AGTTGAAGTT
Statistics
Matches: 143, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
61 7 0.05
63 118 0.83
65 18 0.13
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (63 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCATTGCGATTTATTCCAAATTCG
Found at i:38694 original size:105 final size:105
Alignment explanation
Indices: 38527--38797 Score: 461
Period size: 105 Copynumber: 2.6 Consensus size: 105
38517 ATTGCGATAG
*
38527 TCCAAGTTCGCATTGCGATAGTCGAAGTTCACGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
1 TCCAAGTTCG--TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTAT
* *
38592 TTCAAATTCGTTGTGATAGTCCAAGTTCGCGTCGCGATTTAT
64 TCCAAATTCGTTGCGATAGTCCAAGTTCGCGTCGCGATTTAT
* *
38634 TCCAAGTTCGTTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATTCATTGCGATTTATTC
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTC
*
38699 CAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
66 CAAATTCGTTGCGATAGTCCAAGTTCGCGTCGCGATTTAT
*
38739 TCCAAGTTCGTTGCGATAGTTGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGAT
38798 AGTCCAAAAT
Statistics
Matches: 155, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
105 145 0.94
107 10 0.06
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (105 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATTTATTC
CAAATTCGTTGCGATAGTCCAAGTTCGCGTCGCGATTTAT
Found at i:38798 original size:42 final size:42
Alignment explanation
Indices: 38686--38804 Score: 211
Period size: 42 Copynumber: 2.8 Consensus size: 42
38676 TCCAAATTCA
38686 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
1 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
* **
38728 TTGCGATTTATTCCAAGTTCGTTGCGATAGTTGAAGTTCGCG
1 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
38770 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
38805 AATCGCAACG
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 71 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (42 bp):
TTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCG
Found at i:39561 original size:42 final size:42
Alignment explanation
Indices: 39496--39741 Score: 286
Period size: 42 Copynumber: 5.9 Consensus size: 42
39486 CGTTGCGATT
* * * *
39496 TTGGACTATCG-AACGAAGTTGGAATAAATCGTAATGCGAAC
1 TTGGACAATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* * * *
39537 TTCGACCATCGCAGCGAATTTGGAATAAATCG--ACGCGAAT
1 TTGGACAATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
39577 TTGGAATAAATCGCAACGAAATTGGAATAAATCGCAA--CGAAC
1 TTGG-A-CAATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
39619 TTGGAATAAATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGG-A-CAATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
*
39663 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACAATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
39705 TTGGACTATCGCAACGAATTTGGAATAAATCGTAACG
1 TTGGACAATCGCAACGAATTTGGAATAAATCGCAACG
39742 AATTTGGAAT
Statistics
Matches: 181, Mismatches: 17, Indels: 13
0.86 0.08 0.06
Matches are distributed among these distances:
40 9 0.05
41 10 0.06
42 151 0.83
43 1 0.01
44 10 0.06
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.22
Consensus pattern (42 bp):
TTGGACAATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:39574 original size:21 final size:21
Alignment explanation
Indices: 39544--39772 Score: 261
Period size: 21 Copynumber: 10.8 Consensus size: 21
39534 AACTTCGACC
* *
39544 ATCGCAGCGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
39565 ATCG-ACGCGAATTTGGAATAA
1 ATCGCA-ACGAACTTGGAATAA
*
39586 ATCGCAACGAAATTGGAATAA
1 ATCGCAACGAACTTGGAATAA
39607 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
39628 ATCGCAACGAACTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
39649 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
39670 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
*
39691 ATCGCAACGCGAACTTGGACT--
1 ATCGCAA--CGAACTTGGAATAA
*
39712 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
* *
39733 ATCGTAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGAATAA
39754 ATCGCAACGCGAACTTGGA
1 ATCGCAA--CGAACTTGGA
39773 CTATCGCAAT
Statistics
Matches: 183, Mismatches: 13, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
19 20 0.11
20 1 0.01
21 131 0.72
22 1 0.01
23 30 0.16
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAACGAACTTGGAATAA
Found at i:39773 original size:63 final size:64
Alignment explanation
Indices: 39544--39781 Score: 303
Period size: 63 Copynumber: 3.8 Consensus size: 64
39534 AACTTCGACC
* *
39544 ATCGCAGCGAATTTGGAATAAATCG--ACGCGAATTTGGAATAAATCGCAACGAAATTGGAATAA
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAAT-AATCGCAACGAAATTGGAATAA
* * *
39607 ATCGCAACGAACTTGGAATAAATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTGGACT
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAAT-AATCGCAA--CGAAATTGGAAT
39670 --
63 AA
* *
39670 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT-ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAATCGCAACGAAATTGGAATAA
* *
39733 ATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTGGACT-ATCGCAA
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAATCGCAA
39782 TGCGAATATG
Statistics
Matches: 157, Mismatches: 10, Indels: 16
0.86 0.05 0.09
Matches are distributed among these distances:
61 10 0.06
63 125 0.80
65 22 0.14
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (64 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGAATAATCGCAACGAAATTGGAATAA
Found at i:40672 original size:5 final size:5
Alignment explanation
Indices: 40662--40697 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
40652 TTTCGCAAAT
*
40662 ATAAA ATAAA ATAAA ATAAA ATAAA ACAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
40698 GTGAAAAGCG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
ATAAA
Found at i:40682 original size:15 final size:15
Alignment explanation
Indices: 40657--40697 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
40647 GCAATTTTCG
40657 CAAATATAAAATAAAA
1 CAAA-ATAAAATAAAA
*
40673 TAAAATAAAATAAAA
1 CAAAATAAAATAAAA
40688 CAAAATAAAA
1 CAAAATAAAA
40698 GTGAAAAGCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 20 0.87
16 3 0.13
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (15 bp):
CAAAATAAAATAAAA
Found at i:42515 original size:3 final size:3
Alignment explanation
Indices: 42498--42565 Score: 93
Period size: 3 Copynumber: 22.0 Consensus size: 3
42488 TTGGGCCTAC
*
42498 ATA ATA AGTA TTA ATA ATA ATTA ATA ATA A-A AGTA ATA ATA ATA ATA
1 ATA ATA A-TA ATA ATA ATA A-TA ATA ATA ATA A-TA ATA ATA ATA ATA
42545 ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA
42566 TGAAAATAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
2 2 0.03
3 50 0.85
4 7 0.12
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:42980 original size:136 final size:130
Alignment explanation
Indices: 42776--43258 Score: 388
Period size: 131 Copynumber: 3.7 Consensus size: 130
42766 TCGTCTAAGA
* * * *
42776 GTGACACAACTCCTATGTGATGAGGAGATCTGGTCGATGGATGACACTATTCCTACGTGATGAGG
1 GTGACAC-ACTCCTACGTGATGAGGAGGTCTGGTCGATGAATGACACTATTCCTACATGATGAGG
* * *
42841 ATGGCTTGACCATCTTTAAGAAATGG-TGACAACACAGTTCCTACGCGATGAGGACGACTGGTTA
65 ATGGC-AGACCATCTTT-AG----GGATGACAACACAGTTCCTACACGATGAGGACAACTGGTTA
42905 TCTAGGG
124 TCTAGGG
* *
42912 GTGACACGACTCGTACGTGATGAGGAGGTCTGGTCGATGAATGACAC-AGTTCTTACATGATGAG
1 GTGACAC-ACTCCTACGTGATGAGGAGGTCTGGTCGATGAATGACACTA-TTCCTACATGATGAG
* * * *
42976 GATGGCAGACCATCTTTAGGGATGATAACACGGTTCCTACATGATGAGTACAACTGGTTATCTAG
64 GATGGCAGACCATCTTTAGGGATGACAACACAGTTCCTACACGATGAGGACAACTGGTTATCTAG
43041 GG
129 GG
* ** * * * *
43043 GTAACACAGCTCCTACGTGATGAGGAGGTCTGGTCAGGGGGATGAAACAATTCCTACACGATGAG
1 GTGACACA-CTCCTACGTGATGAGGAGGTCTGGTC-GATGAATGACACTATTCCTACATGATGAG
* ** * * * * ** * ** * *
43108 GACGATAGGCTATATTTA-GG--GACGACATGGTTCCTTCGTGATGAGGACGACTCGTTATCT-G
64 GATGGCAGACCATCTTTAGGGATGACAACACAGTTCCTACACGATGAGGACAACTGGTTATCTAG
*
43169 AAG
129 -GG
* * * ** * *
43172 TTGACACGACTCCTACGTGATGAAGAGGTCTAGTCGGGGGATGACA-TGGTTCCTACATGATGAG
1 GTGACAC-ACTCCTACGTGATGAGGAGGTCTGGTCGATGAATGACACT-ATTCCTACATGATGAG
*
43236 GATGACATG-CCATCTTTAGGGAT
64 GATGGCA-GACCATCTTTAGGGAT
43259 ATTGTTTCAA
Statistics
Matches: 286, Mismatches: 49, Indels: 29
0.79 0.13 0.08
Matches are distributed among these distances:
128 37 0.13
129 65 0.23
130 4 0.01
131 72 0.25
132 33 0.12
133 1 0.00
134 2 0.01
135 11 0.04
136 61 0.21
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (130 bp):
GTGACACACTCCTACGTGATGAGGAGGTCTGGTCGATGAATGACACTATTCCTACATGATGAGGA
TGGCAGACCATCTTTAGGGATGACAACACAGTTCCTACACGATGAGGACAACTGGTTATCTAGGG
Found at i:43464 original size:68 final size:69
Alignment explanation
Indices: 43364--43501 Score: 165
Period size: 68 Copynumber: 2.0 Consensus size: 69
43354 TTTTTCAAGG
* * * * *
43364 GAAACTGTCTTAAGGGAGACAAAATTCGTTTAAAAGGAAACGACTCAAAGA-TG-ATTTTGTTTT
1 GAAAATGTCTTAAGAGAGAAAAAATTCGTTTAAAAGAAAAAGACTCAAAGATTGAATTTTGTTTT
43427 TAGA
66 TAGA
*
43431 GAAAATGTCTTAAGAGAGAAAAAAATT-GTTTTAAGAGAAAAAGACTCAAAGATTGTCAATTTTG
1 GAAAATGTCTTAAGAGAG-AAAAAATTCG-TTTAAAAGAAAAAGACTCAAAGATTG--AATTTTG
43495 TTTTTAG
62 TTTTTAG
43502 TTAAACAACT
Statistics
Matches: 59, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
67 17 0.29
68 27 0.46
69 2 0.03
72 13 0.22
ACGTcount: A:0.41, C:0.08, G:0.20, T:0.31
Consensus pattern (69 bp):
GAAAATGTCTTAAGAGAGAAAAAATTCGTTTAAAAGAAAAAGACTCAAAGATTGAATTTTGTTTT
TAGA
Found at i:43465 original size:21 final size:19
Alignment explanation
Indices: 43432--43472 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
43422 GTTTTTAGAG
43432 AAAATGTCTTAAGAGAGAAA
1 AAAATGTCTTAAGAGA-AAA
*
43452 AAAATTGTTTTAAGAGAAAA
1 AAAA-TGTCTTAAGAGAAAA
43472 A
1 A
43473 GACTCAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.24
Consensus pattern (19 bp):
AAAATGTCTTAAGAGAAAA
Found at i:43674 original size:33 final size:36
Alignment explanation
Indices: 43628--43723 Score: 101
Period size: 38 Copynumber: 2.7 Consensus size: 36
43618 ATCTCAGAAA
*
43628 AAATGTCTCAAGCGA-A-ACAA-T-TTTTTTTAGAG
1 AAATGTCTCAAGCGAGACAAAATTGTTTTTTTAGAG
43660 AAATAGTCTCAAGCGAGACAAAATTTGTTTTTTTAGAG
1 AAAT-GTCTCAAGCGAGACAAAA-TTGTTTTTTTAGAG
* *
43698 AAAGTTGTCTCAAGCAATACAAAATT
1 AAA--TGTCTCAAGCGAGACAAAATT
43724 TATTTATAAG
Statistics
Matches: 53, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
32 4 0.08
33 11 0.21
34 1 0.02
35 3 0.06
37 1 0.02
38 16 0.30
39 16 0.30
40 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (36 bp):
AAATGTCTCAAGCGAGACAAAATTGTTTTTTTAGAG
Found at i:43696 original size:38 final size:39
Alignment explanation
Indices: 43649--43724 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
43639 GCGAAACAAT
*
43649 TTTTTTTAGAGAAA-TAGTCTCAAGCGAGACAAAATTTG
1 TTTTTTTAGAGAAAGTAGTCTCAAGCAAGACAAAATTTG
* *
43687 TTTTTTTAGAGAAAGTTGTCTCAAGCAATACAAAATTT
1 TTTTTTTAGAGAAAGTAGTCTCAAGCAAGACAAAATTT
43725 ATTTATAAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 14 0.41
39 20 0.59
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (39 bp):
TTTTTTTAGAGAAAGTAGTCTCAAGCAAGACAAAATTTG
Found at i:44114 original size:16 final size:16
Alignment explanation
Indices: 44093--44132 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
44083 TTCATATATC
* *
44093 ATGTATGTATGTGTTG
1 ATGTATGTATATATTG
*
44109 ATGTATGTTTATATTG
1 ATGTATGTATATATTG
44125 ATGTATGT
1 ATGTATGT
44133 TTTCTTGATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.53
Consensus pattern (16 bp):
ATGTATGTATATATTG
Found at i:45142 original size:2 final size:2
Alignment explanation
Indices: 45135--45161 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45125 TCAAATTTAT
45135 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 T
45162 TTGTTTACGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50131 original size:23 final size:23
Alignment explanation
Indices: 50097--50156 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
50087 CATTTTATAT
*
50097 GGCACTTTGGTGCAATTCTACGC
1 GGCACTTAGGTGCAATTCTACGC
* *
50120 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTAGGTGCAATTCTACGC
*
50143 GGTACTTAGGTGCA
1 GGCACTTAGGTGCA
50157 TTTATACGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.30
Consensus pattern (23 bp):
GGCACTTAGGTGCAATTCTACGC
Found at i:50164 original size:23 final size:23
Alignment explanation
Indices: 50096--50164 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
50086 ACATTTTATA
* *
50096 TGGCACTTTGGTGCAATTCTACG
1 TGGCACTTAGGTGCAATTATACG
* * *
50119 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTAGGTGCAATTATACG
* *
50142 TGGTACTTAGGTGCATTTATACG
1 TGGCACTTAGGTGCAATTATACG
50165 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.33
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTATACG
Found at i:53084 original size:2 final size:2
Alignment explanation
Indices: 53077--53112 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
53067 AACATAGATG
53077 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
53113 AGTTTAAGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:58713 original size:5 final size:5
Alignment explanation
Indices: 58703--58733 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
58693 TTTTGCAAAG
*
58703 ATAAA ATAAA ATAAA ATAAA ACAAA ATAAA A
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA A
58734 GTGAAAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (5 bp):
ATAAA
Found at i:60575 original size:3 final size:3
Alignment explanation
Indices: 60561--60659 Score: 164
Period size: 3 Copynumber: 33.0 Consensus size: 3
60551 ACATGTATTG
* *
60561 ATA ATA ATTA ATA ATA AGA GTA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
60607 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
60654 ATA ATA
1 ATA ATA
60660 TGAAAATAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.02
3 85 0.94
4 3 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:67201 original size:27 final size:27
Alignment explanation
Indices: 67162--67218 Score: 78
Period size: 27 Copynumber: 2.1 Consensus size: 27
67152 TCAAACCTGA
* *
67162 TAACGTCTCAATAGTAAGGCCCATGCC
1 TAACGTCTCAATAGCAAGGCCCACGCC
* *
67189 TAACGTCTTAATAGCGAGGCCCACGCC
1 TAACGTCTCAATAGCAAGGCCCACGCC
67216 TAA
1 TAA
67219 ACTACCCAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (27 bp):
TAACGTCTCAATAGCAAGGCCCACGCC
Found at i:67646 original size:31 final size:27
Alignment explanation
Indices: 67611--67691 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
67601 AAAAAGTTGA
67611 GTCGGGTGGAGGGTATATATTTTTCGGTCGG
1 GTCGGGTGGAGGGTATATATTTTT---T-GG
* * * * *
67642 GTCGGGTGAAGGATGTAAAATTTTTGG
1 GTCGGGTGGAGGGTATATATTTTTTGG
67669 GTCGGGTGGAGGGTATATATTTT
1 GTCGGGTGGAGGGTATATATTTT
67692 CGGCCAACCT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
27 20 0.50
28 1 0.03
31 19 0.47
ACGTcount: A:0.19, C:0.06, G:0.40, T:0.36
Consensus pattern (27 bp):
GTCGGGTGGAGGGTATATATTTTTTGG
Found at i:76193 original size:23 final size:21
Alignment explanation
Indices: 76141--76202 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
76131 TTTTGGTGCA
*
76141 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
76161 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
76182 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
76203 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:76210 original size:21 final size:21
Alignment explanation
Indices: 76184--76223 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
76174 CCCCCTTTGA
*
76184 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
76205 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
76224 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:79634 original size:17 final size:17
Alignment explanation
Indices: 79612--79654 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
79602 TAATTTGATT
*
79612 AATGAACTAGT-TAAATG
1 AATGAACTAGTGT-AATC
79629 AATGAACTAGTGTAATC
1 AATGAACTAGTGTAATC
79646 AATGAACTA
1 AATGAACTA
79655 ATTTTATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.47, C:0.09, G:0.16, T:0.28
Consensus pattern (17 bp):
AATGAACTAGTGTAATC
Found at i:80389 original size:20 final size:20
Alignment explanation
Indices: 80366--80403 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
80356 AATCATTCTA
*
80366 ATTCGTCCAGTATCAATACT
1 ATTCATCCAGTATCAATACT
*
80386 ATTCATCTAGTATCAATA
1 ATTCATCCAGTATCAATA
80404 ATCAAACCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.37
Consensus pattern (20 bp):
ATTCATCCAGTATCAATACT
Found at i:84863 original size:21 final size:19
Alignment explanation
Indices: 84831--84888 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
84821 GTTAATATCG
84831 GAAATAATCATTTTCGGTAA
1 GAAATAA-CATTTTCGGTAA
*
84851 CGAAATTAACATTTCCGGTAA
1 -GAAA-TAACATTTTCGGTAA
*
84872 -AAATAACATTTTAGGTA
1 GAAATAACATTTTCGGTA
84889 GAGCTCTACC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 12 0.36
19 3 0.09
21 15 0.45
22 3 0.09
ACGTcount: A:0.41, C:0.12, G:0.14, T:0.33
Consensus pattern (19 bp):
GAAATAACATTTTCGGTAA
Found at i:85298 original size:31 final size:32
Alignment explanation
Indices: 85229--85289 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
85219 ATATTCAAAG
85229 ATTTTAAAATAAATATCATATATTAATATTAA
1 ATTTTAAAATAAATATCATATATTAATATTAA
*
85261 ATTTTAAAAT-AATGTCATATATTAATATT
1 ATTTTAAAATAAATATCATATATTAATATT
85290 TATCTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 18 0.64
32 10 0.36
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (32 bp):
ATTTTAAAATAAATATCATATATTAATATTAA
Found at i:86409 original size:41 final size:39
Alignment explanation
Indices: 86364--86474 Score: 114
Period size: 41 Copynumber: 3.0 Consensus size: 39
86354 GAGACAACGT
86364 TCGTGTTCGTTTATTTATTTTTAAAGGTGTTCATGTTCGGG
1 TCGTGTTCGTTTATTTATTTTTAAAGGTGTTCATGTTC--G
* *
86405 TCGTGTTCGTTTA---ATTTTTTAA--T-ATCATGTT--
1 TCGTGTTCGTTTATTTATTTTTAAAGGTGTTCATGTTCG
*
86436 T-GTGTTCGTTTATTTATTTTTAAAGGTGTTCGTGTTCG
1 TCGTGTTCGTTTATTTATTTTTAAAGGTGTTCATGTTCG
86474 T
1 T
86475 TCATTTAACG
Statistics
Matches: 57, Mismatches: 5, Indels: 19
0.70 0.06 0.23
Matches are distributed among these distances:
30 11 0.19
31 1 0.02
33 8 0.14
35 8 0.14
36 7 0.12
38 9 0.16
41 13 0.23
ACGTcount: A:0.15, C:0.09, G:0.21, T:0.55
Consensus pattern (39 bp):
TCGTGTTCGTTTATTTATTTTTAAAGGTGTTCATGTTCG
Found at i:87256 original size:20 final size:20
Alignment explanation
Indices: 87231--87269 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
87221 TCTGGTTTCA
87231 AGTATCGATATTGGATGAAC
1 AGTATCGATATTGGATGAAC
*
87251 AGTATCGATATTGGTTGAA
1 AGTATCGATATTGGATGAA
87270 TTGGGACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (20 bp):
AGTATCGATATTGGATGAAC
Found at i:89168 original size:23 final size:23
Alignment explanation
Indices: 89140--89231 Score: 103
Period size: 23 Copynumber: 4.0 Consensus size: 23
89130 GGATGTTATA
* *
89140 CGTTTAACATTCGTGAATATGTT
1 CGTTTAACGTTCGTGAACATGTT
* *
89163 TGTTTAACGTTTGTGAACATGTT
1 CGTTTAACGTTCGTGAACATGTT
* *
89186 CATTTAACGTTCGTAAACATGTT
1 CGTTTAACGTTCGTGAACATGTT
* * *
89209 CGTTTAGCGTTTGTGAAAATGTT
1 CGTTTAACGTTCGTGAACATGTT
89232 AAAAAATGTT
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.43
Consensus pattern (23 bp):
CGTTTAACGTTCGTGAACATGTT
Found at i:89208 original size:46 final size:46
Alignment explanation
Indices: 89142--89231 Score: 126
Period size: 46 Copynumber: 2.0 Consensus size: 46
89132 ATGTTATACG
* * * *
89142 TTTAACATTCGTGAATATGTTTGTTTAACGTTTGTGAACATGTTCA
1 TTTAACATTCGTAAACATGTTCGTTTAACGTTTGTGAAAATGTTCA
* *
89188 TTTAACGTTCGTAAACATGTTCGTTTAGCGTTTGTGAAAATGTT
1 TTTAACATTCGTAAACATGTTCGTTTAACGTTTGTGAAAATGTT
89232 AAAAAATGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.44
Consensus pattern (46 bp):
TTTAACATTCGTAAACATGTTCGTTTAACGTTTGTGAAAATGTTCA
Found at i:89506 original size:16 final size:17
Alignment explanation
Indices: 89470--89510 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
89460 GGGTCAATCC
89470 CAACAAAATCAAGAAAA
1 CAACAAAATCAAGAAAA
* *
89487 CAACAAAATC-ATACAA
1 CAACAAAATCAAGAAAA
89503 CAACAAAA
1 CAACAAAA
89511 AACCCAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 12 0.55
17 10 0.45
ACGTcount: A:0.68, C:0.22, G:0.02, T:0.07
Consensus pattern (17 bp):
CAACAAAATCAAGAAAA
Found at i:91332 original size:15 final size:15
Alignment explanation
Indices: 91312--91357 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
91302 TGAGTCGGTC
91312 GAGTCAACTCAGACT
1 GAGTCAACTCAGACT
91327 GAGTCAA-T----C-
1 GAGTCAACTCAGACT
91336 GAGTCAACTCAGACT
1 GAGTCAACTCAGACT
91351 GAGTCAA
1 GAGTCAA
91358 TCGAGTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
9 7 0.28
10 2 0.08
14 2 0.08
15 14 0.56
ACGTcount: A:0.35, C:0.24, G:0.22, T:0.20
Consensus pattern (15 bp):
GAGTCAACTCAGACT
Found at i:91386 original size:29 final size:24
Alignment explanation
Indices: 91265--91370 Score: 160
Period size: 24 Copynumber: 4.4 Consensus size: 24
91255 CTTGATACCA
**
91265 AGTCAACTC-GAACTGAGTTGATCG
1 AGTCAACTCAG-ACTGAGTCAATCG
**
91289 AGTCAACTCAGACTGAGTCGGTCG
1 AGTCAACTCAGACTGAGTCAATCG
91313 AGTCAACTCAGACTGAGTCAATCG
1 AGTCAACTCAGACTGAGTCAATCG
91337 AGTCAACTCAGACTGAGTCAATCG
1 AGTCAACTCAGACTGAGTCAATCG
91361 AGTCAACTCA
1 AGTCAACTCA
91371 AATCGAACTG
Statistics
Matches: 77, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
24 76 0.99
25 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.23, T:0.22
Consensus pattern (24 bp):
AGTCAACTCAGACTGAGTCAATCG
Found at i:99427 original size:13 final size:13
Alignment explanation
Indices: 99408--99459 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
99398 GTATTGTCGG
99408 AAATATTATTTTT
1 AAATATTATTTTT
* *
99421 TAATATT-TTTGAT
1 AAATATTATTT-TT
*
99434 AAATATTA-TTTA
1 AAATATTATTTTT
99446 AAATATTATTTTT
1 AAATATTATTTTT
99459 A
1 A
99460 TCGAAAATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (13 bp):
AAATATTATTTTT
Found at i:99561 original size:76 final size:75
Alignment explanation
Indices: 99419--99561 Score: 202
Period size: 78 Copynumber: 1.9 Consensus size: 75
99409 AATATTATTT
* *
99419 TTTAATATTTTTGATAAATATTATTTAAAATATTATTTTTATCGAAAATTTTAATATTAGACGTT
1 TTTAATATTTTTGATAAATATTATCTAAAATATTATTTTTATCGAAAATATTAATATTAGACGTT
99484 ATTTAAAATG
66 ATTTAAAATG
*
99494 TTTAATATTTTTGATAAA-ACGTTATCTAAAATATTATTTTTTTATCGGAAATATTAATATT-GA
1 TTTAATATTTTTGATAAATA--TTATCTAAAATATTA--TTTTTATCGAAAATATTAATATTAGA
99557 -GTTAT
62 CGTTAT
99562 ACCGAAAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
74 1 0.02
75 18 0.30
76 19 0.31
77 2 0.03
78 21 0.34
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.50
Consensus pattern (75 bp):
TTTAATATTTTTGATAAATATTATCTAAAATATTATTTTTATCGAAAATATTAATATTAGACGTT
ATTTAAAATG
Found at i:100051 original size:60 final size:61
Alignment explanation
Indices: 99987--100123 Score: 147
Period size: 60 Copynumber: 2.3 Consensus size: 61
99977 AATATTTTCG
* *
99987 TTTCATCCTTAAATTATGATTTTCATTCTAAATTAGTCCTCAAA-ATTTTGAACATCTC-AT
1 TTTCATCC-TAAATTATGATCTTCATTCTAAATTAGTCCCCAAACATTTTGAACATCTCAAT
** * * * *
100047 TTTCATCC-CCATGCTATGATCTTCATTCTAAATTGGTCCCCAAACTTTTTGAATATTTCAAT
1 TTTCATCCTAAAT--TATGATCTTCATTCTAAATTAGTCCCCAAACATTTTGAACATCTCAAT
100109 TTT-ATCCTAAATTAT
1 TTTCATCCTAAATTAT
100124 TCATATGTAC
Statistics
Matches: 62, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
58 2 0.03
60 38 0.61
61 15 0.24
62 7 0.11
ACGTcount: A:0.29, C:0.20, G:0.06, T:0.45
Consensus pattern (61 bp):
TTTCATCCTAAATTATGATCTTCATTCTAAATTAGTCCCCAAACATTTTGAACATCTCAAT
Found at i:100347 original size:60 final size:60
Alignment explanation
Indices: 100268--100397 Score: 172
Period size: 60 Copynumber: 2.2 Consensus size: 60
100258 TGGAAGACCT
* * * *
100268 AAAAGTTTAGGGACCAATTTAGAATGTGA-TTCATAGTTTGAGGATGAAATTTAAATGTTC
1 AAAAGTTTAAGGACCAATTTAGAATGAGAGTT-ATAGTTTAAGGATGAAATTGAAATGTTC
* * *
100328 AAAAGTTTAAGGACTAATTTAGAATGAGAGTTATAGTTTAAGGATGAAATTGGAATGTTT
1 AAAAGTTTAAGGACCAATTTAGAATGAGAGTTATAGTTTAAGGATGAAATTGAAATGTTC
*
100388 AAAAGCTTAA
1 AAAAGTTTAA
100398 AGCTTAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 59 0.97
61 2 0.03
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.34
Consensus pattern (60 bp):
AAAAGTTTAAGGACCAATTTAGAATGAGAGTTATAGTTTAAGGATGAAATTGAAATGTTC
Found at i:101567 original size:15 final size:15
Alignment explanation
Indices: 101500--101567 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
101490 ATATTTAGTT
* *
101500 GGGCGGGCGGATGTG
1 GGGCGGGTGGATGCG
101515 GGGCGGGTGGATGCG
1 GGGCGGGTGGATGCG
* ***
101530 GGTCGGACAGATGCG
1 GGGCGGGTGGATGCG
*
101545 GGGCGGGTGGATACG
1 GGGCGGGTGGATGCG
101560 GGGCGGGT
1 GGGCGGGT
101568 AAGGTCTCAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.10, C:0.15, G:0.62, T:0.13
Consensus pattern (15 bp):
GGGCGGGTGGATGCG
Found at i:104485 original size:17 final size:18
Alignment explanation
Indices: 104460--104496 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
104450 TAAATATAAA
104460 AATAACATTATCA-TTTT
1 AATAACATTATCAGTTTT
*
104477 AATATCATTATCAGTTTT
1 AATAACATTATCAGTTTT
104495 AA
1 AA
104497 AAATGTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.41, C:0.11, G:0.03, T:0.46
Consensus pattern (18 bp):
AATAACATTATCAGTTTT
Done.