Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397261.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_50.0, 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: 9139585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 37885 characters in sequence are not A, C, G, or T
File 6 of 19
Found at i:1797005 original size:27 final size:27
Alignment explanation
Indices: 1796938--1797005 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
1796928 CCATCCACAA
**
1796938 TTCTGGT-AAGTAAAAGTATCTATTCAC
1 TTCTGGTGAA-TAAAAGTATCTACCCAC
* * **
1796965 TTCAGATGGGTAAAAGTATCTACCCAC
1 TTCTGGTGAATAAAAGTATCTACCCAC
1796992 TTCTGGTGAATAAA
1 TTCTGGTGAATAAA
1797006 GGTAGCCATC
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (27 bp):
TTCTGGTGAATAAAAGTATCTACCCAC
Found at i:1798551 original size:15 final size:15
Alignment explanation
Indices: 1798531--1798605 Score: 64
Period size: 15 Copynumber: 5.0 Consensus size: 15
1798521 TAATATTATA
1798531 ATTAAAATAAAAAAT
1 ATTAAAATAAAAAAT
*
1798546 ATTAAAATAAAATAT
1 ATTAAAATAAAAAAT
*
1798561 A-TAATAT-AAAAAT
1 ATTAAAATAAAAAAT
** *
1798574 AAAAAAATAAAATAAA
1 ATTAAAATAAAA-AAT
*
1798590 ATAAAAATATAAAAAT
1 ATTAAAATA-AAAAAT
1798606 TAACATTTAT
Statistics
Matches: 48, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
13 6 0.12
14 9 0.19
15 18 0.38
16 12 0.25
17 3 0.06
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
ATTAAAATAAAAAAT
Found at i:1798556 original size:5 final size:5
Alignment explanation
Indices: 1798533--1798595 Score: 53
Period size: 5 Copynumber: 13.0 Consensus size: 5
1798523 ATATTATAAT
* * *
1798533 TAAAA TAAAA -AATAT TAAAA TAAAA T-ATA TAATA TAAAA -ATAAA -AAAA
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA
1798581 TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA
1798596 ATATAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
4 9 0.18
5 38 0.78
6 2 0.04
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:1798588 original size:13 final size:13
Alignment explanation
Indices: 1798533--1798603 Score: 65
Period size: 13 Copynumber: 5.4 Consensus size: 13
1798523 ATATTATAAT
1798533 TAAAATAAAAAATA
1 TAAAATAAAAAA-A
*
1798547 TTAAAAT-AAAATA
1 -TAAAATAAAAAAA
* *
1798560 TATAATATAAAAA
1 TAAAATAAAAAAA
1798573 TAAAA-AAATAAAA
1 TAAAATAAA-AAAA
*
1798586 TAAAATAAAAATA
1 TAAAATAAAAAAA
1798599 TAAAA
1 TAAAA
1798604 ATTAACATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
12 7 0.15
13 26 0.57
14 7 0.15
15 6 0.13
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAAAAAAA
Found at i:1798605 original size:8 final size:8
Alignment explanation
Indices: 1798534--1798605 Score: 57
Period size: 8 Copynumber: 9.6 Consensus size: 8
1798524 TATTATAATT
1798534 AAAATA-A
1 AAAATATA
1798541 AAAATAT-
1 AAAATATA
*
1798548 TAAA-AT-
1 AAAATATA
1798554 AAAATAT-
1 AAAATATA
*
1798561 ATAATATA
1 AAAATATA
*
1798569 AAAATAAA
1 AAAATATA
1798577 AAAATA-A
1 AAAATATA
*
1798584 AATAAAATA
1 AA-AATATA
1798593 AAAATATA
1 AAAATATA
1798601 AAAAT
1 AAAAT
1798606 TAACATTTAT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
6 5 0.09
7 20 0.38
8 25 0.47
9 3 0.06
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATATA
Found at i:1798688 original size:33 final size:32
Alignment explanation
Indices: 1798638--1798722 Score: 82
Period size: 33 Copynumber: 2.5 Consensus size: 32
1798628 AAACAAATTA
*
1798638 AAATAAAATATATAATATAAAAAA-TATATTAAAG
1 AAATAAAATA-A-AATATAAAAAATTATAAT-AAG
* * *
1798672 AAATGAAAATAAAATATATAAGATTATAATAAT
1 AAAT-AAAATAAAATATAAAAAATTATAATAAG
1798705 AAATAAAAATAAAATATA
1 AAAT-AAAATAAAATATA
1798723 TGACATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
33 28 0.64
34 10 0.23
35 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (32 bp):
AAATAAAATAAAATATAAAAAATTATAATAAG
Found at i:1798779 original size:21 final size:22
Alignment explanation
Indices: 1798755--1798828 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
1798745 ATATGATATT
1798755 ATATAAAA-ATTAATAATATAA
1 ATATAAAATATTAATAATATAA
*
1798776 ATATAAATATATTAAAAATA-AA
1 ATATAAA-ATATTAATAATATAA
1798798 ATATAAAATATT-ATAATAATAA
1 ATATAAAATATTAATAAT-ATAA
1798820 ATA-AAAATA
1 ATATAAAATA
1798829 AAATATATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.09
21 19 0.40
22 15 0.32
23 9 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
ATATAAAATATTAATAATATAA
Found at i:1798780 original size:6 final size:6
Alignment explanation
Indices: 1798769--1798835 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
1798759 AAAAATTAAT
* *
1798769 AATATA AATATA AATAT- ATTAAA AATA-A AATATAA AATATTA TAATAATA
1 AATATA AATATA AATATA AATATA AATATA AATAT-A AATA-TA -AAT-ATA
*
1798819 AATAAA AATA-A AATATA
1 AATATA AATATA AATATA
1798836 TGACATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
5 13 0.26
6 21 0.42
7 9 0.18
8 6 0.12
9 1 0.02
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AATATA
Found at i:1798817 original size:113 final size:114
Alignment explanation
Indices: 1798677--1798905 Score: 406
Period size: 113 Copynumber: 2.0 Consensus size: 114
1798667 TAAAGAAATG
*
1798677 AAAATAAAATATATAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
* *
1798742 AAGATATGATATTATATAAAAATTAATAAT-ATAAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
*
1798790 AAAATAAAATATAAAATATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
1 AAAATAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
*
1798855 AAGAAATGATATTATATAAAACTTAATAATAAAAAATATAAATATATTA
66 AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
1798904 AA
1 AA
1798906 CTTGTATTTT
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
113 91 0.83
114 19 0.17
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.33
Consensus pattern (114 bp):
AAAATAAAATATAAAAGATTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTT
AAGAAATGATATTATATAAAAATTAATAATAAAAAATATAAATATATTA
Found at i:1799074 original size:15 final size:15
Alignment explanation
Indices: 1799054--1799095 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1799044 ATTTTCCCTA
1799054 CAATCACATTGCTTG
1 CAATCACATTGCTTG
*
1799069 CAATCACATTACTTG
1 CAATCACATTGCTTG
*
1799084 TAATCACATTGC
1 CAATCACATTGC
1799096 ATTGTAATGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.31, C:0.26, G:0.10, T:0.33
Consensus pattern (15 bp):
CAATCACATTGCTTG
Found at i:1799907 original size:29 final size:29
Alignment explanation
Indices: 1799854--1799913 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1799844 AATATTTAAG
*
1799854 TAAATCATTATTAAGATGTATCAAAAAAA
1 TAAATCATTATTAAAATGTATCAAAAAAA
*
1799883 TAAATCATTA-TAAAATTTATACAAAAAAA
1 TAAATCATTATTAAAATGTAT-CAAAAAAA
1799912 TA
1 TA
1799914 TTACATTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 8 0.29
29 20 0.71
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.32
Consensus pattern (29 bp):
TAAATCATTATTAAAATGTATCAAAAAAA
Found at i:1800772 original size:15 final size:14
Alignment explanation
Indices: 1800752--1800785 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1800742 TAACATATGC
1800752 ATAAATAAAATAAAA
1 ATAAATAAAA-AAAA
*
1800767 ATAAATAAAAAATA
1 ATAAATAAAAAAAA
1800781 ATAAA
1 ATAAA
1800786 AAATATATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAATAAAAAAAA
Found at i:1800780 original size:17 final size:17
Alignment explanation
Indices: 1800758--1800790 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
1800748 ATGCATAAAT
1800758 AAAATAA-AAATAAATAA
1 AAAATAATAAA-AAATAA
1800775 AAAATAATAAAAAATA
1 AAAATAATAAAAAATA
1800791 TATAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAATAATAAAAAATAA
Found at i:1800785 original size:25 final size:25
Alignment explanation
Indices: 1800755--1800805 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1800745 CATATGCATA
1800755 AATAAAATAA-AAATAAATAAAAAAT
1 AATAAAA-AATAAATAAATAAAAAAT
* *
1800780 AATAAAAAATATATAATTAAAAAAT
1 AATAAAAAATAAATAAATAAAAAAT
1800805 A
1 A
1800806 TTTTATATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (25 bp):
AATAAAAAATAAATAAATAAAAAAT
Found at i:1800789 original size:21 final size:22
Alignment explanation
Indices: 1800754--1800805 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 22
1800744 ACATATGCAT
1800754 AAATAAAATAAAAATAAATAAA
1 AAATAAAATAAAAATAAATAAA
1800776 AAATAATAA-AAAATATATAATTAAA
1 AAATAA-AATAAAA-ATA-AA-TAAA
1800801 AAATA
1 AAATA
1800806 TTTTATATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
22 10 0.38
23 5 0.19
24 2 0.08
25 9 0.35
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (22 bp):
AAATAAAATAAAAATAAATAAA
Found at i:1800883 original size:19 final size:19
Alignment explanation
Indices: 1800859--1800902 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1800849 AAAATATATA
1800859 TTATGCTCCGCCCCTGCTT
1 TTATGCTCCGCCCCTGCTT
1800878 TTATGCTCCGCCCCTGCTT
1 TTATGCTCCGCCCCTGCTT
*
1800897 GTATGC
1 TTATGC
1800903 ATTAACTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.07, C:0.39, G:0.18, T:0.36
Consensus pattern (19 bp):
TTATGCTCCGCCCCTGCTT
Found at i:1801563 original size:14 final size:15
Alignment explanation
Indices: 1801544--1801576 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1801534 TTAGTTGATG
1801544 TTTTTACTCTTTTT-
1 TTTTTACTCTTTTTC
*
1801558 TTTTTATTCTTTTTC
1 TTTTTACTCTTTTTC
1801573 TTTT
1 TTTT
1801577 GGCAAAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTTACTCTTTTTC
Found at i:1801928 original size:18 final size:18
Alignment explanation
Indices: 1801901--1801940 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1801891 AATTATTAAT
*
1801901 TTATGAGTTATTTATAAA
1 TTATGAGTTAGTTATAAA
* *
1801919 TTATGTGTTAGTTATAAG
1 TTATGAGTTAGTTATAAA
1801937 TTAT
1 TTAT
1801941 TTGTGAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.53
Consensus pattern (18 bp):
TTATGAGTTAGTTATAAA
Found at i:1802651 original size:22 final size:22
Alignment explanation
Indices: 1802623--1802694 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
1802613 AGGCATTGCT
* *
1802623 TAAAAATTAATTACGCAATGTC
1 TAAAAATCAATCACGCAATGTC
*
1802645 TAAAAATCAATCATGCAATGT-
1 TAAAAATCAATCACGCAATGTC
* * * * *
1802666 TTATAACCAATCACGTAATGTT
1 TAAAAATCAATCACGCAATGTC
1802688 TAAAAAT
1 TAAAAAT
1802695 TAGTCTCGTA
Statistics
Matches: 38, Mismatches: 11, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
21 16 0.42
22 22 0.58
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (22 bp):
TAAAAATCAATCACGCAATGTC
Found at i:1802803 original size:2 final size:2
Alignment explanation
Indices: 1802796--1802823 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1802786 AACCTAAAAC
1802796 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
1802824 TTGCTAAGTC
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:1814562 original size:84 final size:84
Alignment explanation
Indices: 1814369--1814630 Score: 249
Period size: 84 Copynumber: 3.1 Consensus size: 84
1814359 GCATTTAAGC
* * * *
1814369 AAAGAATGCTCACTGACAACAGAAATGATGATAACCAAAAAGG-CGAAGTTGAGGACTGTACTCC
1 AAAGAGTGCTCATTGACAACAGAAATGATGATAACCAAAATGGTAGAAG-TGAGGACTGTACTCC
*
1814433 AAGGAGACTCAAGTTCAGGA
65 AAGGAGACTCAACTTCAGGA
* * * * * * *
1814453 AAAGAGTGCTCATTAACAACGGAAATGGTGATAACCAAAATGGTAGATGTGAGGAGTTTATTCCA
1 AAAGAGTGCTCATTGACAACAGAAATGATGATAACCAAAATGGTAGAAGTGAGGACTGTACTCCA
1814518 AGGAGACTCAACTTCAGGA
66 AGGAGACTCAACTTCAGGA
** ** * ** * * *
1814537 GGAGAGCT-CTTGTTGACGACAGAAATTCTGATAACCAAAATGGTAGAGGTGAGGACTATACCCC
1 AAAGAG-TGCTCATTGACAACAGAAATGATGATAACCAAAATGGTAGAAGTGAGGACTGTACTCC
* * * *
1814601 AAGGAAACTTAAGTTCAGGC
65 AAGGAGACTCAACTTCAGGA
*
1814621 CAAGAGTGCT
1 AAAGAGTGCT
1814631 TGATCACAGC
Statistics
Matches: 143, Mismatches: 32, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
83 1 0.01
84 138 0.97
85 4 0.03
ACGTcount: A:0.38, C:0.17, G:0.25, T:0.20
Consensus pattern (84 bp):
AAAGAGTGCTCATTGACAACAGAAATGATGATAACCAAAATGGTAGAAGTGAGGACTGTACTCCA
AGGAGACTCAACTTCAGGA
Found at i:1843437 original size:20 final size:23
Alignment explanation
Indices: 1843400--1843444 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
1843390 CATTTAACTA
1843400 TTTATATTTTATGTATTAT-AGT
1 TTTATATTTTATGTATTATAAGT
1843422 TTTATA-TTTA-GTATTATAAGT
1 TTTATATTTTATGTATTATAAGT
1843443 TT
1 TT
1843445 AAATAGCAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 9 0.41
22 6 0.27
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (23 bp):
TTTATATTTTATGTATTATAAGT
Found at i:1860319 original size:2 final size:2
Alignment explanation
Indices: 1860298--1860340 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1860288 CATGGACATG
* * *
1860298 AT AT AC AT AC AT AC 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 AT AT AT AT AT AT
1860340 A
1 A
1860341 ATCATTTTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:1865288 original size:6 final size:7
Alignment explanation
Indices: 1865274--1865298 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1865264 GCTTTTCCAA
1865274 TTTATTT
1 TTTATTT
1865281 TTTATTT
1 TTTATTT
1865288 TTTATTT
1 TTTATTT
1865295 TTTA
1 TTTA
1865299 AAGACTGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTATTT
Found at i:1875929 original size:92 final size:92
Alignment explanation
Indices: 1875772--1875959 Score: 340
Period size: 92 Copynumber: 2.0 Consensus size: 92
1875762 ACTCTTAATA
*
1875772 TTTGGTGTCGCGTGCAACACCTAGAACCATGAATGGAAAAATGTGTTCAAGAAGGGGCTTATTTA
1 TTTGGTGTCGCATGCAACACCTAGAACCATGAATGGAAAAATGTGTTCAAGAAGGGGCTTATTTA
*
1875837 TGTATGCAGCCTCTCTCTTCATCTTGT
66 TATATGCAGCCTCTCTCTTCATCTTGT
* *
1875864 TTTGGTGTTGCATGCAACACCTAGAACCATGAATGGAAAAATGTGTTCAAGGAGGGGCTTATTTA
1 TTTGGTGTCGCATGCAACACCTAGAACCATGAATGGAAAAATGTGTTCAAGAAGGGGCTTATTTA
1875929 TATATGCAGCCTCTCTCTTCATCTTGT
66 TATATGCAGCCTCTCTCTTCATCTTGT
1875956 TTTG
1 TTTG
1875960 CCCATCAAGG
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (92 bp):
TTTGGTGTCGCATGCAACACCTAGAACCATGAATGGAAAAATGTGTTCAAGAAGGGGCTTATTTA
TATATGCAGCCTCTCTCTTCATCTTGT
Found at i:1884563 original size:16 final size:17
Alignment explanation
Indices: 1884542--1884573 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1884532 AAAGCTTTTT
1884542 AATTA-TTTTTTAAAAA
1 AATTATTTTTTTAAAAA
1884558 AATTATTTTTTTAAAA
1 AATTATTTTTTTAAAA
1884574 TTTAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTATTTTTTTAAAAA
Found at i:1888271 original size:19 final size:19
Alignment explanation
Indices: 1888247--1888295 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 19
1888237 ATCTAAATAA
*
1888247 TAAAAAATATTATATATTT
1 TAAAAAATATTAAATATTT
1888266 TAAAAAA-A-TAAATATTT
1 TAAAAAATATTAAATATTT
1888283 TCAAAAAAGTATT
1 T-AAAAAA-TATT
1888296 TTTTTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
17 9 0.36
18 7 0.28
19 7 0.28
20 1 0.04
21 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
TAAAAAATATTAAATATTT
Found at i:1888354 original size:6 final size:6
Alignment explanation
Indices: 1888343--1888368 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1888333 TAAATTAATC
1888343 AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA
1888369 CTAGTAAGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:1888494 original size:4 final size:4
Alignment explanation
Indices: 1888485--1888513 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1888475 TCTATTATAG
1888485 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA T
1888514 CAATCAATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:1909629 original size:21 final size:20
Alignment explanation
Indices: 1909600--1909644 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1909590 CTTCAACAGC
*
1909600 ATTACAAAAATGTTACAAAGA
1 ATTACAAAAAT-TCACAAAGA
* *
1909621 ATTAGAAAAATTCATAAAGA
1 ATTACAAAAATTCACAAAGA
1909641 ATTA
1 ATTA
1909645 TCAGATCTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.58, C:0.07, G:0.09, T:0.27
Consensus pattern (20 bp):
ATTACAAAAATTCACAAAGA
Found at i:1916432 original size:22 final size:22
Alignment explanation
Indices: 1916388--1916445 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1916378 TCAAATAATT
* *
1916388 TTTTATTATTATATTTAATTAAAA
1 TTTTA-TATTA-AATTAAATAAAA
*
1916412 TTTTATATTAAATTAAATAAAT
1 TTTTATATTAAATTAAATAAAA
1916434 TTTTATAATTAA
1 TTTTAT-ATTAA
1916446 CAGTTGATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 15 0.50
23 10 0.33
24 5 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATATTAAATTAAATAAAA
Found at i:1926693 original size:2 final size:2
Alignment explanation
Indices: 1926686--1926745 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1926676 CTTAGCTGCT
* *
1926686 TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1926728 TA TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA
1926746 ATCCTCTTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1941976 original size:22 final size:22
Alignment explanation
Indices: 1941950--1941991 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1941940 ATTAAATTTT
*
1941950 TTATTTATAAATAGAATAAATC
1 TTATTAATAAATAGAATAAATC
* *
1941972 TTATTAATAATTATAATAAA
1 TTATTAATAAATAGAATAAA
1941992 AAATATTTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TTATTAATAAATAGAATAAATC
Found at i:1942044 original size:74 final size:74
Alignment explanation
Indices: 1941966--1942107 Score: 225
Period size: 74 Copynumber: 1.9 Consensus size: 74
1941956 ATAAATAGAA
*
1941966 TAAATCTTATTAATAATTATAATAAAAAATATTTCAAG-GATCATCATTT-GATGAATACACATT
1 TAAATCTTACTAATAATTATAATAAAAAATATTTC-AGTGATCATCATTTAG-TGAATACACATT
1942029 TATAATAGGTT
64 TATAATAGGTT
* *
1942040 TAAATCTTACTAATAATTATAATAAAAAATATTTCAGTGATCGTCATTTAGTGAATACATATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAGTGATCATCATTTAGTGAATACACATTTA
1942105 TAA
66 TAA
1942108 ATATAAGTTT
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
73 2 0.03
74 60 0.95
75 1 0.02
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (74 bp):
TAAATCTTACTAATAATTATAATAAAAAATATTTCAGTGATCATCATTTAGTGAATACACATTTA
TAATAGGTT
Found at i:1954426 original size:56 final size:56
Alignment explanation
Indices: 1954340--1954448 Score: 191
Period size: 56 Copynumber: 1.9 Consensus size: 56
1954330 CGCATTCTGG
*
1954340 TGTTATGTTTCATCATGATTAATGTTGTTGAGGCCTATAATTGATTAGCACTATGC
1 TGTTATGTTTCATCATGATTAATGTTGTTGAAGCCTATAATTGATTAGCACTATGC
* *
1954396 TGTTATGTTTCATCATGGTTAATGTTGTTGAAGCCTCTAATTGATTAGCACTA
1 TGTTATGTTTCATCATGATTAATGTTGTTGAAGCCTATAATTGATTAGCACTA
1954449 CGCTATAGGT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 50 1.00
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (56 bp):
TGTTATGTTTCATCATGATTAATGTTGTTGAAGCCTATAATTGATTAGCACTATGC
Found at i:1973550 original size:2 final size:2
Alignment explanation
Indices: 1973543--1973581 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1973533 ATGCATTGAG
1973543 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1973582 GATTAAAAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1975265 original size:2 final size:2
Alignment explanation
Indices: 1975260--1975291 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1975250 GTGTGTACAT
1975260 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1975292 AAGGACCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1988989 original size:23 final size:23
Alignment explanation
Indices: 1988963--1989012 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
1988953 ATTTTTAGGA
* * *
1988963 AAGTTTTCAAAATTGATTCCACT
1 AAGTTTACAAAAGTGATTCAACT
*
1988986 AAG-TTACAAAAGTGATTTAACT
1 AAGTTTACAAAAGTGATTCAACT
1989008 AAGTT
1 AAGTT
1989013 AGCAAAAATG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.36
Consensus pattern (23 bp):
AAGTTTACAAAAGTGATTCAACT
Found at i:1989001 original size:22 final size:23
Alignment explanation
Indices: 1988970--1989019 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
1988960 GGAAAGTTTT
* *
1988970 CAAAATTGATTCCACTAAGTTA-
1 CAAAAGTGATTCAACTAAGTTAG
*
1988992 CAAAAGTGATTTAACTAAGTTAG
1 CAAAAGTGATTCAACTAAGTTAG
1989015 CAAAA
1 CAAAA
1989020 ATGAGTATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (23 bp):
CAAAAGTGATTCAACTAAGTTAG
Found at i:1989031 original size:22 final size:22
Alignment explanation
Indices: 1988983--1989031 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1988973 AATTGATTCC
* *
1988983 ACTAAGTTACAAAAGTGATTTA
1 ACTAAGTTACAAAAATGATGTA
1989005 ACTAAGTTAGCAAAAATGA-GTA
1 ACTAAGTTA-CAAAAATGATGTA
*
1989027 TCTAA
1 ACTAA
1989032 AATCATTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.29
Consensus pattern (22 bp):
ACTAAGTTACAAAAATGATGTA
Found at i:1990301 original size:30 final size:30
Alignment explanation
Indices: 1990241--1990318 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
1990231 ACTGAACATC
*
1990241 CTTGATTCCATT-TTTCATTAAATAGGGTTTT
1 CTTGATTCCATTCTTT--TTAAATAGAGTTTT
*
1990272 CTTGATTCCATTCTTTTTTAATAGAGTTTT
1 CTTGATTCCATTCTTTTTAAATAGAGTTTT
*
1990302 CTTGATTCTATTCTTTT
1 CTTGATTCCATTCTTTT
1990319 CAGATATTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 28 0.65
31 12 0.28
32 3 0.07
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.56
Consensus pattern (30 bp):
CTTGATTCCATTCTTTTTAAATAGAGTTTT
Found at i:1990814 original size:66 final size:65
Alignment explanation
Indices: 1990682--1990828 Score: 172
Period size: 66 Copynumber: 2.2 Consensus size: 65
1990672 TTGCATGTGG
* * * * *
1990682 TTTGTTTTTCATCGGCTACTTCGGTGCCATACTTGATCTCCATCGACTGTTTCGTTGTCACACGT
1 TTTGTTTTTCATTGGCTACTTCGATGCCATACTTGATATCCATCGACTCTTTCCTTGT--CACGT
1990747 GA
64 GA
* *
1990749 TTTGTTTTTCATTGGCTACTTC-ATGCCATACTTGTTATCCATCGACTACTTTGCTCTTGT-GCG
1 TTTGTTTTTCATTGGCTACTTCGATGCCATACTTGATATCCATCGACT-CTTT-C-CTTGTCACG
1990812 TGA
63 TGA
1990815 TTTGTTTTTCATTG
1 TTTGTTTTTCATTG
1990829 ACTATTTTGG
Statistics
Matches: 70, Mismatches: 7, Indels: 7
0.83 0.08 0.08
Matches are distributed among these distances:
66 41 0.59
67 24 0.34
68 1 0.01
69 4 0.06
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (65 bp):
TTTGTTTTTCATTGGCTACTTCGATGCCATACTTGATATCCATCGACTCTTTCCTTGTCACGTGA
Found at i:1990908 original size:67 final size:67
Alignment explanation
Indices: 1990645--1990913 Score: 227
Period size: 67 Copynumber: 4.0 Consensus size: 67
1990635 GCCACACGTG
** * * * *
1990645 ATTTGTTCTTTATCAACTGCTTTGGTGTTGCATGTGGTTTGTTTTTCATCGGCTACTTCGGTGCC
1 ATTTGTTCTCCATCAACTGCTTTGATGTTGCACGTGATTTGTTTTTCATCGACTACTTCGGTGCC
1990710 AT
66 AT
* * * * ** * * *
1990712 ACTTGATCTCCATCGACTG-TTTCGTTGTCACACGTGATTTGTTTTTCATTGGCTACTTC-ATGC
1 ATTTGTTCTCCATCAACTGCTTT-GATGTTGCACGTGATTTGTTTTTCATCGACTACTTCGGTGC
1990775 CAT
65 CAT
* * * * * * ** * * *
1990778 ACTTGTTATCCATCGACTACTTTGCTCTTGTGCGTGATTTGTTTTTCATTGACTATTTTGGTGCC
1 ATTTGTTCTCCATCAACTGCTTTGATGTTGCACGTGATTTGTTTTTCATCGACTACTTCGGTGCC
1990843 AT
66 AT
* * * ** *
1990845 ATTTGTTCTCTATCAATTGCTTTGATGTTGTACGTGATTTGTTTTTTGTCGACTGCTTCGGTGCC
1 ATTTGTTCTCCATCAACTGCTTTGATGTTGCACGTGATTTGTTTTTCATCGACTACTTCGGTGCC
1990910 AT
66 AT
1990912 AT
1 AT
1990914 GTGATTTATT
Statistics
Matches: 159, Mismatches: 40, Indels: 6
0.78 0.20 0.03
Matches are distributed among these distances:
66 52 0.33
67 107 0.67
ACGTcount: A:0.14, C:0.19, G:0.19, T:0.47
Consensus pattern (67 bp):
ATTTGTTCTCCATCAACTGCTTTGATGTTGCACGTGATTTGTTTTTCATCGACTACTTCGGTGCC
AT
Found at i:1990918 original size:36 final size:36
Alignment explanation
Indices: 1990875--1990965 Score: 110
Period size: 36 Copynumber: 2.5 Consensus size: 36
1990865 TTTGATGTTG
* *
1990875 TACGTGATTTGTTTTTTGTCGACTGCTTCGGTGCCA
1 TACGTGATTTGTTCTTTGTCGACTGCTTCGGTACCA
* * * * *
1990911 TATGTGATTTATTCTTTGTCGGCTGCTTTGGTATCA
1 TACGTGATTTGTTCTTTGTCGACTGCTTCGGTACCA
*
1990947 TACGTGATATGTTCTTTGT
1 TACGTGATTTGTTCTTTGT
1990966 TGGTTGCTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.48
Consensus pattern (36 bp):
TACGTGATTTGTTCTTTGTCGACTGCTTCGGTACCA
Found at i:2012042 original size:27 final size:27
Alignment explanation
Indices: 2011994--2012052 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
2011984 TTATTTAATT
*
2011994 TAATTTAATTTAACTTTTAAATGA-TAA
1 TAATTTAATTTAACTTTAAAAT-ATTAA
*
2012021 TAATTTATATTTTA-TTTAAAATATTAA
1 TAATTTA-ATTTAACTTTAAAATATTAA
2012048 TAATT
1 TAATT
2012053 GAAAATTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 1 0.04
27 22 0.79
28 5 0.18
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
TAATTTAATTTAACTTTAAAATATTAA
Found at i:2012075 original size:42 final size:42
Alignment explanation
Indices: 2012022--2012131 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
2012012 AAATGATAAT
* *
2012022 AATTTATATTTTATTTAAAATATTAATAATTGAA-AATTT-AAA
1 AATTAATATTTTATTTAAAAT-TTAATAA-TCAATAATTTGAAA
* * * *
2012064 AATTAATATTTTCTTTATAATTTAATCATCAATATTTTGAAA
1 AATTAATATTTTATTTAAAATTTAATAATCAATAATTTGAAA
* *
2012106 TATTAATATTTTATTTTATAATTTAA
1 AATTAATATTTTA-TTTAAAATTTAA
2012132 ATATTATTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
40 3 0.05
41 10 0.18
42 32 0.56
43 12 0.21
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (42 bp):
AATTAATATTTTATTTAAAATTTAATAATCAATAATTTGAAA
Found at i:2014003 original size:20 final size:21
Alignment explanation
Indices: 2013957--2014005 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
2013947 CAAGGCAAAA
2013957 ATAGAGAGAAGAGTTTTTTAG
1 ATAGAGAGAAGAGTTTTTTAG
* *
2013978 AGAGAGA-AAGA-TTTTTTGGG
1 ATAGAGAGAAGAGTTTTTT-AG
2013998 ATAGAGAG
1 ATAGAGAG
2014006 CATAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 6 0.26
20 11 0.48
21 6 0.26
ACGTcount: A:0.39, C:0.00, G:0.33, T:0.29
Consensus pattern (21 bp):
ATAGAGAGAAGAGTTTTTTAG
Found at i:2020231 original size:48 final size:48
Alignment explanation
Indices: 2020138--2020345 Score: 186
Period size: 48 Copynumber: 4.3 Consensus size: 48
2020128 TTAGGTATTT
* * * * * *
2020138 AATCATTTTAATGTTGCGTAGCTTCGTTTAGAGATGAGAAACTTTTTC
1 AATCATTTTAAAGTTGCATAGCCTCATTTAGAGATAAGAAGCTTTTTC
** * * *
2020186 AATCATTTTAAAGTTGTGTATCCTCATTTAAAGATAAGGAGCTTTTTC
1 AATCATTTTAAAGTTGCATAGCCTCATTTAGAGATAAGAAGCTTTTTC
* * ** *
2020234 AATTATTTTAAAGTTGCATATCCTTGTTTAGAGATAA-AGAGCTTTTCC
1 AATCATTTTAAAGTTGCATAGCCTCATTTAGAGATAAGA-AGCTTTTTC
* * ** * *
2020282 AATTATTTTAACGTTATATAGCTTCATTTAGAGATGAGAAGC-TTTTC
1 AATCATTTTAAAGTTGCATAGCCTCATTTAGAGATAAGAAGCTTTTTC
2020329 TAATCATTTTAAAGTTG
1 -AATCATTTTAAAGTTG
2020346 AGGAGCTTTC
Statistics
Matches: 128, Mismatches: 29, Indels: 6
0.79 0.18 0.04
Matches are distributed among these distances:
47 4 0.03
48 123 0.96
49 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (48 bp):
AATCATTTTAAAGTTGCATAGCCTCATTTAGAGATAAGAAGCTTTTTC
Found at i:2020347 original size:28 final size:28
Alignment explanation
Indices: 2020316--2020373 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
2020306 CATTTAGAGA
*
2020316 TGAGAAGCTTTTCTAATCATTTTAAAGT
1 TGAGAAGCTTTCCTAATCATTTTAAAGT
*
2020344 TGAGGAGCTTTCCTAATCATTTTAAAGT
1 TGAGAAGCTTTCCTAATCATTTTAAAGT
2020372 TG
1 TG
2020374 TAATAGGCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (28 bp):
TGAGAAGCTTTCCTAATCATTTTAAAGT
Found at i:2020531 original size:48 final size:48
Alignment explanation
Indices: 2020336--2020851 Score: 344
Period size: 48 Copynumber: 10.6 Consensus size: 48
2020326 TTCTAATCAT
* * * *
2020336 TTTAAAGTTGAGGAGC-TTTCCTAATCATTTTAAAGTTGTAATAGGCTCG
1 TTTAAAGATGAGGAGCTTTTCC-AATCATTTTAAAGTTGT-GTAGCCTCA
* * *
2020385 TTTAAAGATGATGAGCTTTTCTAATCATTTTAAAGTTGTAAG-AGCCTCT
1 TTTAAAGATGAGGAGCTTTTCCAATCATTTTAAAGTTGT--GTAGCCTCA
* ** * * *
2020434 TTTATAGATGACAAGCTTTTTTCAATCGTTTTAAAGTTGCGTAGCCTCA
1 TTTAAAGATGAGGAGC-TTTTCCAATCATTTTAAAGTTGTGTAGCCTCA
* *
2020483 TTTAAAGATGAAGAGCTTTTCCAATCATTTTAAAGTTGTGTAGTCTCA
1 TTTAAAGATGAGGAGCTTTTCCAATCATTTTAAAGTTGTGTAGCCTCA
* * * ** *
2020531 TTTAGAGATGAGGAG-TTTTCTTAGTCATTTTAAAGTTGCATAGCCTTA
1 TTTAAAGATGAGGAGCTTTTC-CAATCATTTTAAAGTTGTGTAGCCTCA
* * * * ** * *
2020579 TTTAGAGATGTGAAGTTTTTTTAATCATTTTAAAGTTGTAAG-AGCTTCT
1 TTTAAAGATGAGGAGCTTTTCCAATCATTTTAAAGTTGT--GTAGCCTCA
* * ** * * *
2020628 TTTAAAGATGAGGAGCGTTTTTCAATTATTTTAAAGTTGCATAACTTGA
1 TTTAAAGATGAGGAGC-TTTTCCAATCATTTTAAAGTTGTGTAGCCTCA
*** * * *
2020677 TTCGGAGATGAGGAGC-TTTCCTAATCATTTTAAAGTTGTGTTGGCTCC
1 TTTAAAGATGAGGAGCTTTTCC-AATCATTTTAAAGTTGTGTAGCCTCA
* * * **
2020725 TTTAGAA-ATGATGAGTTTTTCTAATCATTTTAAAGTTGTGTAGCCTTG
1 TTTA-AAGATGAGGAGCTTTTCCAATCATTTTAAAGTTGTGTAGCCTCA
* * * * * ** * *
2020773 TTGAGAGATAAGAAGTCTTTTCCAATCATGTTAAAGTCATATAGTCTCA
1 TTTAAAGATGAGGAG-CTTTTCCAATCATTTTAAAGTTGTGTAGCCTCA
* * *
2020822 TTTAGAGATGAGGAG-TTTTCTAATTATTTT
1 TTTAAAGATGAGGAGCTTTTCCAATCATTTT
2020852 TCATTGCCTC
Statistics
Matches: 360, Mismatches: 92, Indels: 32
0.74 0.19 0.07
Matches are distributed among these distances:
47 22 0.06
48 148 0.41
49 146 0.41
50 44 0.12
ACGTcount: A:0.29, C:0.11, G:0.19, T:0.41
Consensus pattern (48 bp):
TTTAAAGATGAGGAGCTTTTCCAATCATTTTAAAGTTGTGTAGCCTCA
Found at i:2020695 original size:194 final size:194
Alignment explanation
Indices: 2020344--2020809 Score: 533
Period size: 194 Copynumber: 2.4 Consensus size: 194
2020334 ATTTTAAAGT
* * * * * *
2020344 TGAGGAGCTTTCCTAATCATTTTAAAGTTGTAATAGGCTCGTTTAAAGATGATG-AGCTTTTCTA
1 TGAGGAGTTTTCTTAATCATTTTAAAGTTG-AATAGCCTTGTTTAGAGATG-TGAAGTTTTTCTA
* * *
2020408 ATCATTTTAAAGTTGTAAGAGCCTCTTTTATAGATGACAAGCTTTTTTCAATCGTTTTAAAGTTG
64 ATCATTTTAAAGTTGTAAGAGCCTCTTTTAAAGATGACAAGCGTTTTTCAATCATTTTAAAGTTG
* * * *
2020473 CGTAGCCTCATTTAAAGATGAAGAGCTTTTCC-AATCATTTTAAAGTTGTGTAGTCTCATTTAGA
129 CATAACCTCATTCAAAGATGAAGAGC-TTTCCTAATCATTTTAAAGTTGTGTAGGCTCATTTAGA
*
2020537 GA
193 AA
* * * *
2020539 TGAGGAGTTTTCTTAGTCATTTTAAAGTTGCATAGCCTTATTTAGAGATGTGAAGTTTTTTTAAT
1 TGAGGAGTTTTCTTAATCATTTTAAAGTTGAATAGCCTTGTTTAGAGATGTGAAGTTTTTCTAAT
* ** *
2020604 CATTTTAAAGTTGTAAGAGCTTCTTTTAAAGATGAGGAGCGTTTTTCAATTATTTTAAAGTTGCA
66 CATTTTAAAGTTGTAAGAGCCTCTTTTAAAGATGACAAGCGTTTTTCAATCATTTTAAAGTTGCA
* * ** * * *
2020669 TAACTTGATTCGGAGATGAGGAGCTTTCCTAATCATTTTAAAGTTGTGTTGGCTCCTTTAGAAA
131 TAACCTCATTCAAAGATGAAGAGCTTTCCTAATCATTTTAAAGTTGTGTAGGCTCATTTAGAAA
* ** * ** *
2020733 TGATGAGTTTT-TCTAATCATTTTAAAGTTGTGTAGCCTTGTTGAGAGATAAGAAGTCTTTTCCA
1 TGAGGAGTTTTCT-TAATCATTTTAAAGTTGAATAGCCTTGTTTAGAGATGTGAAGT-TTTTCTA
*
2020797 ATCATGTTAAAGT
64 ATCATTTTAAAGT
2020810 CATATAGTCT
Statistics
Matches: 227, Mismatches: 40, Indels: 8
0.83 0.15 0.03
Matches are distributed among these distances:
193 8 0.04
194 175 0.77
195 44 0.19
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (194 bp):
TGAGGAGTTTTCTTAATCATTTTAAAGTTGAATAGCCTTGTTTAGAGATGTGAAGTTTTTCTAAT
CATTTTAAAGTTGTAAGAGCCTCTTTTAAAGATGACAAGCGTTTTTCAATCATTTTAAAGTTGCA
TAACCTCATTCAAAGATGAAGAGCTTTCCTAATCATTTTAAAGTTGTGTAGGCTCATTTAGAAA
Found at i:2020833 original size:194 final size:192
Alignment explanation
Indices: 2020488--2020851 Score: 441
Period size: 194 Copynumber: 1.9 Consensus size: 192
2020478 CCTCATTTAA
* *
2020488 AGATGAAGAGCTTTTCCAATCATTTTAAAGTTGTGTAGTCTCATTTAGAGATGAGGAGTTTTCTT
1 AGATGAAGAGCTTTTCCAATCATTTTAAAGTTGTGTAGGCTCATTTAGAAATGAGGAGTTTTCTT
* * ** ** * **
2020553 AGTCATTTTAAAGTTGCATAGCCTTATTTAGAGATGTGAAGTTTTTTTAATCATTTTAAAGTTGT
66 AATCATTTTAAAGTTGCATAGCCTTATTGAGAGATAAGAAGTTTTTCCAATCATGTTAAAGTCAT
*
2020618 AAGAGCTTCTTTTAAAGATGAGGAGCGTTTT-TCAATTATTTTAAAGTTGCATAACTTGATTCGG
131 AAGAGCTTCATTTAAAGATGAGGA--GTTTTCT-AATTATTTTAAAGTTGCATAACTTGATTCGG
* * * *
2020682 AGATGAGGAGC-TTTCCTAATCATTTTAAAGTTGTGTTGGCTCCTTTAGAAATGATGAGTTTT-T
1 AGATGAAGAGCTTTTCC-AATCATTTTAAAGTTGTGTAGGCTCATTTAGAAATGAGGAGTTTTCT
** *
2020745 CTAATCATTTTAAAGTTGTGTAGCCTTGTTGAGAGATAAGAAGTCTTTTCCAATCATGTTAAAGT
65 -TAATCATTTTAAAGTTGCATAGCCTTATTGAGAGATAAGAAGT-TTTTCCAATCATGTTAAAGT
* *
2020810 CAT-ATAG-TCTCATTTAGAGATGAGGAGTTTTCTAATTATTTT
128 CATAAGAGCT-TCATTTAAAGATGAGGAGTTTTCTAATTATTTT
2020852 TCATTGCCTC
Statistics
Matches: 144, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
192 14 0.10
193 8 0.06
194 104 0.72
195 18 0.12
ACGTcount: A:0.29, C:0.10, G:0.20, T:0.41
Consensus pattern (192 bp):
AGATGAAGAGCTTTTCCAATCATTTTAAAGTTGTGTAGGCTCATTTAGAAATGAGGAGTTTTCTT
AATCATTTTAAAGTTGCATAGCCTTATTGAGAGATAAGAAGTTTTTCCAATCATGTTAAAGTCAT
AAGAGCTTCATTTAAAGATGAGGAGTTTTCTAATTATTTTAAAGTTGCATAACTTGATTCGG
Found at i:2021090 original size:6 final size:6
Alignment explanation
Indices: 2021081--2021109 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2021071 AAAAAGAAAA
2021081 GATAAT GATAAT GATAAT GATAAT GATAA
1 GATAAT GATAAT GATAAT GATAAT GATAA
2021110 AAGCAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.17, T:0.31
Consensus pattern (6 bp):
GATAAT
Found at i:2028438 original size:13 final size:13
Alignment explanation
Indices: 2028403--2028441 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
2028393 TATAATTTAC
*
2028403 TAATTAAAATACA
1 TAATTAAAATATA
*
2028416 TAATAAAAATATA
1 TAATTAAAATATA
*
2028429 TAATTTAAATATA
1 TAATTAAAATATA
2028442 ATGAGAACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATTAAAATATA
Found at i:2028876 original size:28 final size:28
Alignment explanation
Indices: 2028802--2028907 Score: 95
Period size: 29 Copynumber: 3.7 Consensus size: 28
2028792 TCAACTTTTA
** * *
2028802 AAAAGTATTTATCAATTTCTAGTGGGTC
1 AAAAGTATCCATCAACTTCTAATGGGTC
**
2028830 AAAAAGTATCCATTTACTTCTAATGGGTC
1 -AAAAGTATCCATCAACTTCTAATGGGTC
* * **
2028859 AAAATTATCCATCAACTTCTGATGACTC
1 AAAAGTATCCATCAACTTCTAATGGGTC
*
2028887 ATAAAGTATCCATCTACTTCT
1 A-AAAGTATCCATCAACTTCT
2028908 GATGCAAAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
28 23 0.37
29 39 0.63
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (28 bp):
AAAAGTATCCATCAACTTCTAATGGGTC
Found at i:2028908 original size:29 final size:28
Alignment explanation
Indices: 2028831--2028911 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
2028821 TAGTGGGTCA
* * **
2028831 AAAAGTATCCATTTACTTCTAATGGGTC
1 AAAAGTATCCATCTACTTCTGATGACTC
* *
2028859 AAAATTATCCATCAACTTCTGATGACTC
1 AAAAGTATCCATCTACTTCTGATGACTC
2028887 ATAAAGTATCCATCTACTTCTGATG
1 A-AAAGTATCCATCTACTTCTGATG
2028912 CAAAATTATC
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
28 23 0.52
29 21 0.48
ACGTcount: A:0.33, C:0.21, G:0.11, T:0.35
Consensus pattern (28 bp):
AAAAGTATCCATCTACTTCTGATGACTC
Found at i:2028970 original size:27 final size:28
Alignment explanation
Indices: 2028913--2028970 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
2028903 CTTCTGATGC
* * *
2028913 AAAATTATCTGTCAACTTTTGGTGCGTT
1 AAAATTATCTATCAACTTTTCGTGCGGT
2028941 AAAATTATCTATCAA-TTTTCG-GCGAGT
1 AAAATTATCTATCAACTTTTCGTGCG-GT
2028968 AAA
1 AAA
2028971 TGTATTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 3 0.12
27 9 0.35
28 14 0.54
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (28 bp):
AAAATTATCTATCAACTTTTCGTGCGGT
Found at i:2029609 original size:2 final size:2
Alignment explanation
Indices: 2029602--2029631 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2029592 GAATATTCAC
*
2029602 AT AT AT AT AT AT AT AT AT AT AA AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2029632 TCATAACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2033515 original size:2 final size:2
Alignment explanation
Indices: 2033508--2033543 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2033498 AGAATAGTTG
2033508 AT AT AT 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 AT AT AT
2033544 GAGGAAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2034187 original size:28 final size:29
Alignment explanation
Indices: 2034151--2034224 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
2034141 GAGTTAAACA
* *
2034151 CTTTAAACATGACATGTAATAA-TTTTTT
1 CTTTCAACATGACATGTAACAACTTTTTT
* *
2034179 CTTTCAACACGGCATGTAACAACTTTTTT
1 CTTTCAACATGACATGTAACAACTTTTTT
* *
2034208 -TTTCAATATGCCATGTA
1 CTTTCAACATGACATGTA
2034225 GCTTAGTTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
28 32 0.84
29 6 0.16
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (29 bp):
CTTTCAACATGACATGTAACAACTTTTTT
Found at i:2034637 original size:69 final size:70
Alignment explanation
Indices: 2034518--2034717 Score: 206
Period size: 77 Copynumber: 2.8 Consensus size: 70
2034508 AGTAAAGTTC
* * ** ** *
2034518 AATGCTATCACATAACTTTAGGAATTTCTTTTAAAGTAGGAAACTGTTTCCTATGAAT-TTTCTA
1 AATGCTATC-CTTAATTTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTATGAATCACTCAA
2034582 AATTAA
65 AATTAA
*
2034588 AATGCTATCCTTAATTTTATGAATTTCTTTTAAAGTAGGAAACAATTTCCTGCTCTTTATGAATC
1 AATGCTATCCTTAATTTTAGGAATTTCTTTTAAAGTAGGAAACAA-TT--T-C-C--TATGAATC
2034653 ACTCAAAATTAA
59 ACTCAAAATTAA
* * *
2034665 AATTCTATCCTTAATTTT-GGAAATTGCTTTCAAAGTAGGAAACAATTTCCTAT
1 AATGCTATCCTTAATTTTAGG-AATTTCTTTTAAAGTAGGAAACAATTTCCTAT
2034718 TCTTTATCAA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
69 31 0.28
70 14 0.13
72 2 0.02
73 2 0.02
74 2 0.02
76 10 0.09
77 48 0.44
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (70 bp):
AATGCTATCCTTAATTTTAGGAATTTCTTTTAAAGTAGGAAACAATTTCCTATGAATCACTCAAA
ATTAA
Found at i:2034708 original size:77 final size:77
Alignment explanation
Indices: 2034581--2034744 Score: 231
Period size: 77 Copynumber: 2.1 Consensus size: 77
2034571 TGAATTTTCT
* * * *
2034581 AAATTAAAATGCTATCCTTAATTTTATGAATTTCTTTTAAAGTAGGAAACAATTTCCTGCTCTTT
1 AAATTAAAATGCTATCCTTAATTTTAGGAATTGCTTTCAAAGTAGGAAACAATTTCCTACTCTTT
* *
2034646 ATGAATCACTCA
66 ATCAATCACCCA
* *
2034658 AAATTAAAATTCTATCCTTAATTTT-GGAAATTGCTTTCAAAGTAGGAAACAATTTCCTATTCTT
1 AAATTAAAATGCTATCCTTAATTTTAGG-AATTGCTTTCAAAGTAGGAAACAATTTCCTACTCTT
2034722 TATCAATCACCCA
65 TATCAATCACCCA
*
2034735 AAACTAAAAT
1 AAATTAAAAT
2034745 AGATGGCATT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
76 1 0.01
77 76 0.99
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (77 bp):
AAATTAAAATGCTATCCTTAATTTTAGGAATTGCTTTCAAAGTAGGAAACAATTTCCTACTCTTT
ATCAATCACCCA
Found at i:2053658 original size:13 final size:13
Alignment explanation
Indices: 2053640--2053664 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2053630 GTCCTCAGGC
2053640 CAAAAGTTCCCAG
1 CAAAAGTTCCCAG
2053653 CAAAAGTTCCCA
1 CAAAAGTTCCCA
2053665 TATAGTTTCT
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:0.40, C:0.32, G:0.12, T:0.16
Consensus pattern (13 bp):
CAAAAGTTCCCAG
Found at i:2061504 original size:42 final size:42
Alignment explanation
Indices: 2061440--2061525 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
2061430 CAATTCGGGA
* * *
2061440 TGAGGTTGCTCCTAACACTGAGGTTGTTCCTGCTGTTGAAGT
1 TGAGGTTGCTCCTAACAATGAGGCTATTCCTGCTGTTGAAGT
* * *
2061482 TGAGGTTGTTCCTGACAATGAGGCTATTCTTGCTGTTGAAGT
1 TGAGGTTGCTCCTAACAATGAGGCTATTCCTGCTGTTGAAGT
2061524 TG
1 TG
2061526 TTCTTAAGGC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.17, C:0.16, G:0.29, T:0.37
Consensus pattern (42 bp):
TGAGGTTGCTCCTAACAATGAGGCTATTCCTGCTGTTGAAGT
Found at i:2062548 original size:88 final size:88
Alignment explanation
Indices: 2062431--2062670 Score: 383
Period size: 88 Copynumber: 2.7 Consensus size: 88
2062421 ACATTAATGA
** *
2062431 TGAATTATGGTCAAAGATCAAGCGATATAGCTTGCGACCAATAATATAATATCATTACAGTCAAA
1 TGAATTATGGTCAAAGATTGAGCGATATAGCTTGCGACCAATAATATAATATCATTACAGCCAAA
* *
2062496 TCATGAGCAATAAAGCTAGCGGC
66 TCATGAGCAATAAAGCTAACAGC
*
2062519 TGAATTATGGTCAAAGATTGAGCGATATAGCTTACGACCAATAATATAATATCATTACAGCCAAA
1 TGAATTATGGTCAAAGATTGAGCGATATAGCTTGCGACCAATAATATAATATCATTACAGCCAAA
* *
2062584 TTATGAGCGATAAAGCTAACAGC
66 TCATGAGCAATAAAGCTAACAGC
*
2062607 TGAATTATGGTCAAAGATTGAGCGATATAGCTTGCGACCAATAATATAATA-CAATTGCAGCCAA
1 TGAATTATGGTCAAAGATTGAGCGATATAGCTTGCGACCAATAATATAATATC-ATTACAGCCAA
2062671 GATATAAGTA
Statistics
Matches: 141, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
87 1 0.01
88 140 0.99
ACGTcount: A:0.40, C:0.16, G:0.18, T:0.26
Consensus pattern (88 bp):
TGAATTATGGTCAAAGATTGAGCGATATAGCTTGCGACCAATAATATAATATCATTACAGCCAAA
TCATGAGCAATAAAGCTAACAGC
Found at i:2064744 original size:29 final size:29
Alignment explanation
Indices: 2064710--2064794 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
2064700 TAATAAAGAA
*
2064710 AAGCTGTACGTGAACAGGTACAAGAGAGG
1 AAGCTGTACATGAACAGGTACAAGAGAGG
* *
2064739 AAGCTGTACATGAACAGGTATAAGAGA-A
1 AAGCTGTACATGAACAGGTACAAGAGAGG
* * *
2064767 AAGGTTGTACATGAACAAGTATAAGAGA
1 AA-GCTGTACATGAACAGGTACAAGAGA
2064795 ACAAGGAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
28 2 0.04
29 48 0.96
ACGTcount: A:0.44, C:0.11, G:0.28, T:0.18
Consensus pattern (29 bp):
AAGCTGTACATGAACAGGTACAAGAGAGG
Found at i:2064795 original size:29 final size:30
Alignment explanation
Indices: 2064743--2064800 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
2064733 GAGAGGAAGC
*
2064743 TGTACATGAACAGGTATAAGAGAA-AAGGT
1 TGTACATGAACAAGTATAAGAGAACAAGGT
2064772 TGTACATGAACAAGTATAAGAGAACAAGG
1 TGTACATGAACAAGTATAAGAGAACAAGG
2064801 AAAAAGCAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.47, C:0.09, G:0.26, T:0.19
Consensus pattern (30 bp):
TGTACATGAACAAGTATAAGAGAACAAGGT
Found at i:2065620 original size:24 final size:25
Alignment explanation
Indices: 2065577--2065631 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
2065567 GCATATGATT
2065577 GTTCATGTATTTTGAATT-AA-TGTA
1 GTTCATGTATTTTG-ATTAAATTGTA
2065601 GTTCATGTATGTATTG-TTAAATTGTA
1 GTTCATGTAT-T-TTGATTAAATTGTA
2065627 GTTCA
1 GTTCA
2065632 CATAACTAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
24 12 0.44
25 3 0.11
26 12 0.44
ACGTcount: A:0.27, C:0.05, G:0.18, T:0.49
Consensus pattern (25 bp):
GTTCATGTATTTTGATTAAATTGTA
Found at i:2068126 original size:14 final size:14
Alignment explanation
Indices: 2068107--2068140 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
2068097 TATTATATAT
2068107 ATAATTAATGATAC
1 ATAATTAATGATAC
2068121 ATAATTAATGATAC
1 ATAATTAATGATAC
2068135 A-AATTA
1 ATAATTA
2068141 TATGTTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.35
Consensus pattern (14 bp):
ATAATTAATGATAC
Found at i:2068273 original size:130 final size:137
Alignment explanation
Indices: 2068044--2068292 Score: 316
Period size: 130 Copynumber: 1.8 Consensus size: 137
2068034 NNNNNNNNNN
* * *
2068044 TAAGTTATAGTAATGCTTATGTATAAATTAAATATATGTATTTTATATTACATTATTATATATAT
1 TAAGTTATAGTAATGCTTATATATAAATTAAATATATGTA--TTATATTACATTA-TAAAGATAT
* *
2068109 AATTAATGATACATAATTAATGATACAAATTATATGTTAAAATGTTTTATATAATCATATAAATA
63 AATTAATGATACATAATTAATGACACAAATTATATGTTAAAATGTTTTACATAATCATATAAATA
2068174 AAGTCTATTA
128 AAGTCTATTA
*
2068184 TAAGTTATAGTAATGCTTATATATAAATTAAATATATGTA-TATA-TA-A-TA-AAAGACT-TTA
1 TAAGTTATAGTAATGCTTATATATAAATTAAATATATGTATTATATTACATTATAAAGA-TATAA
* * * *
2068243 TT-AT-ATATATAATTAATGACATAACTTATATGTTATAATGTTTTACATAA
65 TTAATGATACATAATTAATGACACAAATTATATGTTAAAATGTTTTACATAA
2068293 AAGTTTATAT
Statistics
Matches: 98, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
130 40 0.41
131 2 0.02
132 7 0.07
133 1 0.01
134 2 0.02
135 1 0.01
136 2 0.02
137 4 0.04
140 39 0.40
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (137 bp):
TAAGTTATAGTAATGCTTATATATAAATTAAATATATGTATTATATTACATTATAAAGATATAAT
TAATGATACATAATTAATGACACAAATTATATGTTAAAATGTTTTACATAATCATATAAATAAAG
TCTATTA
Found at i:2069517 original size:23 final size:24
Alignment explanation
Indices: 2069491--2069540 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
2069481 AGCGTAATCA
* *
2069491 TATAAGTAAAATTTAT-TATAAGT
1 TATAAGTAAAACTTATGTATAAAT
*
2069514 TAT-AGTAATACTTATGTATAAAT
1 TATAAGTAAAACTTATGTATAAAT
2069537 TATA
1 TATA
2069541 TATACATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
22 10 0.45
23 12 0.55
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (24 bp):
TATAAGTAAAACTTATGTATAAAT
Found at i:2069565 original size:15 final size:14
Alignment explanation
Indices: 2069535--2069571 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
2069525 TTATGTATAA
2069535 ATTATATA-TACAT
1 ATTATATATTACAT
2069548 ATTATATATTACATT
1 ATTATATATTACA-T
2069563 ATTATATAT
1 ATTATATAT
2069572 ATGTGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 8 0.36
14 4 0.18
15 10 0.45
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTATATATTACAT
Found at i:2069898 original size:17 final size:17
Alignment explanation
Indices: 2069876--2069928 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
2069866 TAGTAATTTT
2069876 TATGTATAAATTAAATA
1 TATGTATAAATTAAATA
*
2069893 TATGTATACA-TAATATA
1 TATGTATAAATTAA-ATA
* *
2069910 TTTGTA-AAATTATATA
1 TATGTATAAATTAAATA
2069926 TAT
1 TAT
2069929 ATTCATAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 10 0.34
17 19 0.66
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (17 bp):
TATGTATAAATTAAATA
Found at i:2073095 original size:17 final size:17
Alignment explanation
Indices: 2073058--2073096 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2073048 ATTTTGGGAT
** *
2073058 TGCTCCCCCTAAGTATG
1 TGCTCCCCCTAAACATA
2073075 TGCTCCCCCTAAACATA
1 TGCTCCCCCTAAACATA
2073092 TGCTC
1 TGCTC
2073097 TAATAAAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.13, T:0.28
Consensus pattern (17 bp):
TGCTCCCCCTAAACATA
Found at i:2090986 original size:26 final size:25
Alignment explanation
Indices: 2090957--2091011 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
2090947 TGGAATATTC
2090957 AGCACCAATAGAAAATA-AATAAGGAA
1 AGCACC-ATA-AAAATATAATAAGGAA
* *
2090983 AGCAGCATAACAATATAATAAGGAA
1 AGCACCATAAAAATATAATAAGGAA
2091008 AGCA
1 AGCA
2091012 GGAGTGTCGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 5 0.19
25 16 0.62
26 5 0.19
ACGTcount: A:0.58, C:0.13, G:0.16, T:0.13
Consensus pattern (25 bp):
AGCACCATAAAAATATAATAAGGAA
Found at i:2098384 original size:29 final size:30
Alignment explanation
Indices: 2098350--2098407 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
2098340 AGAACTAAAT
*
2098350 AAATATGAAAATATAATTTT-AAAATAATC
1 AAATATGAAAAGATAATTTTGAAAATAATC
* *
2098379 AAATATGAAAAGCTAATTTTGAATATAAT
1 AAATATGAAAAGATAATTTTGAAAATAAT
2098408 TAAGTAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.34
Consensus pattern (30 bp):
AAATATGAAAAGATAATTTTGAAAATAATC
Found at i:2102362 original size:237 final size:237
Alignment explanation
Indices: 2101981--2102948 Score: 1045
Period size: 237 Copynumber: 4.1 Consensus size: 237
2101971 CACGCCAAAT
* * * *
2101981 AGAAGAAATTTATTATTATTACACACTATGCAGAACAAGTAAAATGTTGTTACACGCCATGCCTA
1 AGAAGAAATTTATTATTGTTACACACTATACAGACCAAATAAAATGTTGTTACACGCCATGCCTA
** * * * * *
2102046 GCTGTTCTTGCATGCTTAA-TTTAATGACTTATTTGTTACATGCCATGAATAAAATATCCACGTT
66 TATGTTCTTACACG-TCAAGTTTAATGACTTATTTGTTACACGCCATGAATAAAATACCCACGTT
* * ** * *
2102110 GTTACATGATATGCCATGCCAAGTATGTGGTTTACACACTACATACCATACATGTAATGCTAAGA
130 GTTACGTGCTATGCCATGCCAAGTATGCAGTTTACACACTACACACCATACATATAATGCTAAGA
* * * * *
2102175 TACACTTAAAAATAGTTAACCCACTTAAAGAAACATGCCAGAA
195 TACACCTAAAAACAGTTAACCCACTCAAAGAAACAAGCTAGAA
* * * * *
2102218 AGAAAAAATTTAGTT-TTGTTACACTCTATGCAGACCAAATAAAATGTTGTTATAGGCCATGCCT
1 AGAAGAAATTTA-TTATTGTTACACACTATACAGACCAAATAAAATGTTGTTACACGCCATGCCT
* * * *
2102282 ATATGTTCTTACATGTCAAGTGTAACGACTTATTTGTTACACGGCATGAATAAAATACCCACGTT
65 ATATGTTCTTACACGTCAAGTTTAATGACTTATTTGTTACACGCCATGAATAAAATACCCACGTT
** ** ** *
2102347 GTTACGTGCTATGCCATGCTGAGTATGC-GATTTACACACTACATGCCACCCATGTAATGCTAAG
130 GTTACGTGCTATGCCATGCCAAGTATGCAG-TTTACACACTACACACCATACATATAATGCTAAG
* * * *
2102411 ATACA--TAAAAAACAGTTAACTCACTCGAAGAAACACGCTAGAT
194 ATACACCT-AAAAACAGTTAACCCACTCAAAGAAACAAGCTAGAA
** * * *
2102454 AGAAGAAATTTATTATTGTTACATGCTATACAGACTAAATAAAATGTTGTTACATGCTATGCCTA
1 AGAAGAAATTTATTATTGTTACACACTATACAGACCAAATAAAATGTTGTTACACGCCATGCCTA
* * *
2102519 TATGTTCTTACACG-CTAAGTTTAATTACTTGTTTGTTACACGCCATGAATGAAATACCCACGTT
66 TATGTTCTTACACGTC-AAGTTTAATGACTTATTTGTTACACGCCATGAATAAAATACCCACGTT
* *** * ** *
2102583 GTTGCGCATTATGCCATGCCAAGTATGCAGTATACACACTACACGTCATACATATAATGCTAAGC
130 GTTACGTGCTATGCCATGCCAAGTATGCAGTTTACACACTACACACCATACATATAATGCTAAGA
* * *
2102648 TACACCCAAAAACAGTCAACCCACTCGAAGAAACAAGCTAGATA
195 TACACCTAAAAACAGTTAACCCACTCAAAGAAACAAGCTAGA-A
* * * * *
2102692 A-AAGAAATTTATTATTGTTATACACTATACAAACCAAATAAAATATTGTTATACGTCATGCCTA
1 AGAAGAAATTTATTATTGTTACACACTATACAGACCAAATAAAATGTTGTTACACGCCATGCCTA
* ** * * * *
2102756 TATGTTCTTATACACCAAGTTTAATTACTTATTTATTACACGTCATGAATGAAATACCCACGTTG
66 TATGTTCTTACACGTCAAGTTTAATGACTTATTTGTTACACGCCATGAATAAAATACCCACGTTG
** * * * * *
2102821 TTACAG-GCTATGCCATGCTGAGTATGTAGTTTACACACTAAACATCATATATATAATGCTAAGC
131 TTAC-GTGCTATGCCATGCCAAGTATGCAGTTTACACACTACACACCATACATATAATGCTAAGA
* * * *
2102885 TACACCTAAAAACAATTAACCCACTCAAATAAACACA-CTGGAT
195 TACACCTAAAAACAGTTAACCCACTCAAAGAAACA-AGCTAGAA
2102928 AGAAGAAATTTATTATTGTTA
1 AGAAGAAATTTATTATTGTTA
2102949 AATGTTATGC
Statistics
Matches: 621, Mismatches: 96, Indels: 28
0.83 0.13 0.04
Matches are distributed among these distances:
235 4 0.01
236 197 0.32
237 414 0.67
238 6 0.01
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (237 bp):
AGAAGAAATTTATTATTGTTACACACTATACAGACCAAATAAAATGTTGTTACACGCCATGCCTA
TATGTTCTTACACGTCAAGTTTAATGACTTATTTGTTACACGCCATGAATAAAATACCCACGTTG
TTACGTGCTATGCCATGCCAAGTATGCAGTTTACACACTACACACCATACATATAATGCTAAGAT
ACACCTAAAAACAGTTAACCCACTCAAAGAAACAAGCTAGAA
Found at i:2102836 original size:473 final size:470
Alignment explanation
Indices: 2101969--2102962 Score: 1194
Period size: 473 Copynumber: 2.1 Consensus size: 470
2101959 GATAATGTGC
* * * ** *
2101969 AACACGCCAAATAGAAGAAATTTATTATTATTACACACTATGCAGAACAAGTAAAATGTTGTTAC
1 AACACGCTAGATAGAAGAAATTTATTATTGTTACATGCTATGCAG-ACAAATAAAATGTTGTTAC
* * * *
2102034 ACGCCATGCCTAGCTGTTCTTGCATGCTTAATTTAATGACTTATTTGTTACATGCCATGAATAAA
65 ACGCCATGCCTAGATGTTCTTACACGCTTAATTTAATGACTTATTTGTTACACGCCATGAATAAA
* ** * * *
2102099 ATATCCACGTTGTTACATGATATGCCATGCCAAGTATGTGGTTTACACACTACATACCATACATG
130 ATACCCACGTTGTTACAT-ATATGCCATGCCAAGTATGCAGTATACACACTACACACCATACATA
** * * * *
2102164 TAATGCTAAGATACACTTAAAAATAGTTAACCCACTTAAAGAAACATGCCAGAAAGAAAAAATTT
194 TAATGCTAAGATACACCCAAAAACAGTCAACCCACTCAAAGAAACAAGCCAGAAAGAAAAAATTT
* * * * *
2102229 AGTTTTGTTACACTCTATGCAGACCAAATAAAATGTTGTTATAGGCCATGCCTATATGTTCTTAC
259 AGTTTTGTTACACACTATACAAACCAAATAAAATATTGTTATACGCCATGCCTATATGTTCTTAC
*** *
2102294 ATGTCAAGTGTAACGACTTATTTGTTACACGGCATGAATAAAATACCCACGTTGTTACGTGCTAT
324 ACACCAAGTGTAACGACTTATTTATTACACGGCATGAATAAAATACCCACGTTGTTACGTGCTAT
* *
2102359 GCCATGCTGAGTATGCGA-TTTACACACT-ACATGCCACCCATGTAATGCTAAGATACA-TAAAA
389 GCCATGCTGAGTATG-GAGTTTACACACTAACAT--CACACATATAATGCTAAGATACACT-AAA
* * *
2102421 AACAGTTAACTCACTCGAAGA
450 AACAATTAACCCACTCAAAGA
*
2102442 AACACGCTAGATAGAAGAAATTTATTATTGTTACATGCTATACAGACTAAATAAAATGTTGTTAC
1 AACACGCTAGATAGAAGAAATTTATTATTGTTACATGCTATGCAGAC-AAATAAAATGTTGTTAC
* * * * * *
2102507 ATGCTATGCCTATATGTTCTTACACGC-TAAGTTTAATTACTTGTTTGTTACACGCCATGAATGA
65 ACGCCATGCCTAGATGTTCTTACACGCTTAA-TTTAATGACTTATTTGTTACACGCCATGAATAA
* **
2102571 AATACCCACGTTGTTGCGCAT-TATGCCATGCCAAGTATGCAGTATACACACTACACGTCATACA
129 AATACCCACGTTGTT--ACATATATGCCATGCCAAGTATGCAGTATACACACTACACACCATACA
* * * *
2102635 TATAATGCTAAGCTACACCCAAAAACAGTCAACCCACTCGAAGAAACAAGCTAGATAA-AAGAAA
192 TATAATGCTAAGATACACCCAAAAACAGTCAACCCACTCAAAGAAACAAGCCAGA-AAGAAAAAA
* *
2102699 TTTA-TTATTGTTATACACTATACAAACCAAATAAAATATTGTTATACGTCATGCCTATATGTTC
256 TTTAGTT-TTGTTACACACTATACAAACCAAATAAAATATTGTTATACGCCATGCCTATATGTTC
* * ** * *
2102763 TTATACACCAAGTTTAATTACTTATTTATTACACGTCATGAATGAAATACCCACGTTGTTACAG-
320 TTACACACCAAGTGTAACGACTTATTTATTACACGGCATGAATAAAATACCCACGTTGTTAC-GT
* * * *
2102827 GCTATGCCATGCTGAGTATGTAGTTTACACACTAAACATCATATATATAATGCTAAGCTACACCT
384 GCTATGCCATGCTGAGTATGGAGTTTACACACT-AACATCACACATATAATGCTAAGATACA-CT
*
2102892 AAAAACAATTAACCCACTCAAATA
447 AAAAACAATTAACCCACTCAAAGA
* * * *
2102916 AACACACTGGATAGAAGAAATTTATTATTGTTAAATGTTATGCAGAC
1 AACACGCTAGATAGAAGAAATTTATTATTGTTACATGCTATGCAGAC
2102963 CCTCTAAAAT
Statistics
Matches: 441, Mismatches: 68, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
472 8 0.02
473 360 0.82
474 65 0.15
475 8 0.02
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (470 bp):
AACACGCTAGATAGAAGAAATTTATTATTGTTACATGCTATGCAGACAAATAAAATGTTGTTACA
CGCCATGCCTAGATGTTCTTACACGCTTAATTTAATGACTTATTTGTTACACGCCATGAATAAAA
TACCCACGTTGTTACATATATGCCATGCCAAGTATGCAGTATACACACTACACACCATACATATA
ATGCTAAGATACACCCAAAAACAGTCAACCCACTCAAAGAAACAAGCCAGAAAGAAAAAATTTAG
TTTTGTTACACACTATACAAACCAAATAAAATATTGTTATACGCCATGCCTATATGTTCTTACAC
ACCAAGTGTAACGACTTATTTATTACACGGCATGAATAAAATACCCACGTTGTTACGTGCTATGC
CATGCTGAGTATGGAGTTTACACACTAACATCACACATATAATGCTAAGATACACTAAAAACAAT
TAACCCACTCAAAGA
Found at i:2104972 original size:66 final size:66
Alignment explanation
Indices: 2104837--2104972 Score: 164
Period size: 66 Copynumber: 2.1 Consensus size: 66
2104827 TTACAAAATT
* ** * * **
2104837 TTGTAACTTTATATATAATATAAATATAATTGAGTTTGAATTTAAAGTACTATGTGCTTGTTTTT
1 TTGTAACATTATATATAATATAAATATAATTGAGTTTGAATTTAAAGTACTAAATGCCTATTTGG
2104902 C
66 C
* * * * *
2104903 TTGTAACATTATATATTATATACATATAATTGGGTTTGAATTTAAGGTATTAAATGCCTATTTGG
1 TTGTAACATTATATATAATATAAATATAATTGAGTTTGAATTTAAAGTACTAAATGCCTATTTGG
2104968 C
66 C
2104969 TTGT
1 TTGT
2104973 TTCTTTTCCT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (66 bp):
TTGTAACATTATATATAATATAAATATAATTGAGTTTGAATTTAAAGTACTAAATGCCTATTTGG
C
Found at i:2106199 original size:2 final size:2
Alignment explanation
Indices: 2106192--2106226 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2106182 TTCAATCACC
2106192 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2106227 CGAGCGATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2108846 original size:4 final size:4
Alignment explanation
Indices: 2108839--2108863 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2108829 TATATATATA
2108839 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
2108864 GTTAAACAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:2113660 original size:15 final size:16
Alignment explanation
Indices: 2113632--2113661 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2113622 TTGCATGTCT
2113632 TTGTCATCCATCATTG
1 TTGTCATCCATCATTG
2113648 TTGTCAT-CATCATT
1 TTGTCATCCATCATT
2113662 TTTGGGGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (16 bp):
TTGTCATCCATCATTG
Found at i:2118795 original size:17 final size:17
Alignment explanation
Indices: 2118764--2118802 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
2118754 TTATTTTATG
**
2118764 TTAATAATTTTTTATAA
1 TTAATAATTAATTATAA
*
2118781 TTAATAATTAATTATTA
1 TTAATAATTAATTATAA
2118798 TTAAT
1 TTAAT
2118803 CAATAAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTAATAATTAATTATAA
Found at i:2124728 original size:22 final size:22
Alignment explanation
Indices: 2124703--2124753 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
2124693 GAATATAAAT
* * *
2124703 TAATTAAAATATAATTTGATAA
1 TAATTAAAAGAAAATTTGAAAA
2124725 TAATTAAAAGAAAATTTGAAAA
1 TAATTAAAAGAAAATTTGAAAA
2124747 TAATTAA
1 TAATTAA
2124754 GTCTCGAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (22 bp):
TAATTAAAAGAAAATTTGAAAA
Found at i:2125805 original size:30 final size:30
Alignment explanation
Indices: 2125742--2125805 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
2125732 ATCCTCTTCA
* *
2125742 TCATGATTTCTATGATCATTTTAAATCTCT
1 TCATGATTTCTATGATAATTTTAAATATCT
* *
2125772 TCATGATTTCTATGATAATTTTGAATATGT
1 TCATGATTTCTATGATAATTTTAAATATCT
2125802 TCAT
1 TCAT
2125806 TAACTTCTTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.50
Consensus pattern (30 bp):
TCATGATTTCTATGATAATTTTAAATATCT
Found at i:2133088 original size:15 final size:15
Alignment explanation
Indices: 2133064--2133094 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2133054 ATTGCATGCT
2133064 AATTAGTTTAGTTTA
1 AATTAGTTTAGTTTA
*
2133079 AATTATTTTAGTTTA
1 AATTAGTTTAGTTTA
2133094 A
1 A
2133095 TTTTTATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (15 bp):
AATTAGTTTAGTTTA
Found at i:2141487 original size:77 final size:77
Alignment explanation
Indices: 2141380--2141548 Score: 198
Period size: 77 Copynumber: 2.2 Consensus size: 77
2141370 TAAATGCAAA
*** * * *
2141380 AAAAAAAGTGATAAGCCAATGCTTGTTAATAAAAATAGATATATAGGCTAATACTAATAT-TATA
1 AAAAAAAGTGATAAGTTGATGTTTGCTAATAAAAATAAATATATAGGCTAATACTAAT-TCTATA
*
2141444 CAAATACTAATGC
65 CAAATACTAATAC
* * *
2141457 AAAGAAAA-TGATAAGTTGATGTTTGCTAATAAAAATAAATATATTGGCTAATTCTAATTCTATG
1 AAA-AAAAGTGATAAGTTGATGTTTGCTAATAAAAATAAATATATAGGCTAATACTAATTCTATA
**
2141521 TGAATACTAATAC
65 CAAATACTAATAC
2141534 AAAAAAAGTGATAAG
1 AAAAAAAGTGATAAG
2141549 CTGTGCAACT
Statistics
Matches: 77, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
76 5 0.06
77 68 0.88
78 4 0.05
ACGTcount: A:0.49, C:0.08, G:0.13, T:0.30
Consensus pattern (77 bp):
AAAAAAAGTGATAAGTTGATGTTTGCTAATAAAAATAAATATATAGGCTAATACTAATTCTATAC
AAATACTAATAC
Found at i:2147403 original size:34 final size:34
Alignment explanation
Indices: 2147347--2147421 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
2147337 GAGTTTTGGT
* * *
2147347 GCTTTGGTTTTGGCATGCAACATCTGGTGCTAAA
1 GCTTTGGTCTTGACATGCAACATCTGATGCTAAA
* * *
2147381 GCTTTGGTCTTGACATGTAACATCTTATGCTGAA
1 GCTTTGGTCTTGACATGCAACATCTGATGCTAAA
2147415 GCTTTGG
1 GCTTTGG
2147422 CCTTAGCTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (34 bp):
GCTTTGGTCTTGACATGCAACATCTGATGCTAAA
Found at i:2147421 original size:76 final size:76
Alignment explanation
Indices: 2147271--2147421 Score: 164
Period size: 76 Copynumber: 2.0 Consensus size: 76
2147261 TAGTGTTGAA
* * * *
2147271 GCTTTGGTTTTGGCATGTAAGATCTAGCACTAAAGCTTTGACCTTGGAGTGTAACATCTACTGTT
1 GCTTTGGTTTTGGCATGCAACATCTAGCACTAAAGCTTTGACCTTGGAATGTAACATCTACTGTC
*
2147336 TGAGTTTTGGT
66 TGAGCTTTGGT
* ** **
2147347 GCTTTGGTTTTGGCATGCAACATCTGGTGCTAAAGCTTTGGTCTT-GACATGTAACATCTTA-TG
1 GCTTTGGTTTTGGCATGCAACATCTAGCACTAAAGCTTTGACCTTGGA-ATGTAACATC-TACTG
2147410 -CTGAAGCTTTGG
64 TCTG-AGCTTTGG
2147422 CCTTAGCTAT
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
75 4 0.06
76 56 0.90
77 2 0.03
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (76 bp):
GCTTTGGTTTTGGCATGCAACATCTAGCACTAAAGCTTTGACCTTGGAATGTAACATCTACTGTC
TGAGCTTTGGT
Found at i:2152186 original size:15 final size:15
Alignment explanation
Indices: 2152166--2152200 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
2152156 TATTAACAAC
2152166 AGTTAATCAATTATT
1 AGTTAATCAATTATT
2152181 AGTTAATCAATTATT
1 AGTTAATCAATTATT
2152196 AGTTA
1 AGTTA
2152201 TAAAGATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.40, C:0.06, G:0.09, T:0.46
Consensus pattern (15 bp):
AGTTAATCAATTATT
Found at i:2152233 original size:25 final size:28
Alignment explanation
Indices: 2152199--2152267 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
2152189 AATTATTAGT
2152199 TATAAAGATTTATTTG-AC-T-TAAAAG
1 TATAAAGATTTATTTGAACATATAAAAG
2152224 TATAAAGATTTGA-TTGAACATAATAAAAG
1 TATAAAGATTT-ATTTGAACAT-ATAAAAG
*
2152253 AATAAAGATTTATTT
1 TATAAAGATTTATTT
2152268 AAATTTTTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
25 14 0.38
26 3 0.08
27 1 0.03
28 1 0.03
29 18 0.49
ACGTcount: A:0.48, C:0.03, G:0.12, T:0.38
Consensus pattern (28 bp):
TATAAAGATTTATTTGAACATATAAAAG
Found at i:2153133 original size:73 final size:74
Alignment explanation
Indices: 2153014--2153153 Score: 255
Period size: 73 Copynumber: 1.9 Consensus size: 74
2153004 ATTATGAACA
2153014 AAATTCCATTTATTAGAATTCACCTTCACGAGCACCTTTATAACTCTGAC-AAAACGACATCGTT
1 AAATTCCATTTATTAGAATTCACCTTCACGAGCACCTTTATAACTCTGACGAAAACGACATCGTT
2153078 TTCGTCATC
66 TTCGTCATC
* *
2153087 AAATTCCATTTATTAGAATTCACCTTCACGAGCGCCTTTATAACTCTGACGGAAACGACATCGTT
1 AAATTCCATTTATTAGAATTCACCTTCACGAGCACCTTTATAACTCTGACGAAAACGACATCGTT
2153152 TT
66 TT
2153154 AACAACGCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
73 49 0.77
74 15 0.23
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (74 bp):
AAATTCCATTTATTAGAATTCACCTTCACGAGCACCTTTATAACTCTGACGAAAACGACATCGTT
TTCGTCATC
Found at i:2184431 original size:34 final size:33
Alignment explanation
Indices: 2184392--2184503 Score: 161
Period size: 34 Copynumber: 3.3 Consensus size: 33
2184382 CAGGAAATTC
*
2184392 ACATCCTTGCACAGTTAAGGTGGTTTTTTAGAAG
1 ACATCCTTGCACAGCTAAGGT-GTTTTTTAGAAG
2184426 ACATCCTTGCACAGCTAAGGTGTTTTTTCAGAAG
1 ACATCCTTGCACAGCTAAGGTGTTTTTT-AGAAG
* * *
2184460 ACATCCTTGCACAGCTAAGTTGTTAATTCAGAAG
1 ACATCCTTGCACAGCTAAGGTGTT-TTTTAGAAG
2184494 ACATCCTTGC
1 ACATCCTTGC
2184504 CCATGGTAAA
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
33 7 0.10
34 63 0.88
35 2 0.03
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.32
Consensus pattern (33 bp):
ACATCCTTGCACAGCTAAGGTGTTTTTTAGAAG
Found at i:2190707 original size:30 final size:30
Alignment explanation
Indices: 2190667--2190723 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
2190657 ATATGGTTTT
*
2190667 AATGGGATTGTGATAACTACCCATTATTTG
1 AATGAGATTGTGATAACTACCCATTATTTG
* *
2190697 AATGAGATTGTGATTATTACCCATTAT
1 AATGAGATTGTGATAACTACCCATTAT
2190724 CTTTAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.39
Consensus pattern (30 bp):
AATGAGATTGTGATAACTACCCATTATTTG
Found at i:2191287 original size:16 final size:17
Alignment explanation
Indices: 2191248--2191287 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2191238 TATTGTATAA
*
2191248 TTATTTTATTTTACGTG
1 TTATTTTATTTTACATG
*
2191265 CTATTTTATTTTA-ATG
1 TTATTTTATTTTACATG
2191281 TTATTTT
1 TTATTTT
2191288 TTCTTTTCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.20, C:0.05, G:0.07, T:0.68
Consensus pattern (17 bp):
TTATTTTATTTTACATG
Found at i:2212526 original size:19 final size:20
Alignment explanation
Indices: 2212482--2212587 Score: 76
Period size: 21 Copynumber: 5.2 Consensus size: 20
2212472 AAATAAATAA
* * *
2212482 ATAAAATTATTTTTTATTAT
1 ATAATATTATATTTTATTTT
2212502 AT-ATATT-TATTTTATTTT
1 ATAATATTATATTTTATTTT
*
2212520 TTAATATTAATATTTTATTTT
1 ATAATATT-ATATTTTATTTT
* *
2212541 ATAAT-TTAATCATTAATATTAT
1 ATAATATT-AT-ATT-TTATTTT
*
2212563 AAAATATTACTATTTTA-TTT
1 ATAATATTA-TATTTTATTTT
2212583 ATAAT
1 ATAAT
2212588 TTAAATATTA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
18 10 0.15
19 9 0.13
20 13 0.19
21 20 0.29
22 13 0.19
23 3 0.04
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (20 bp):
ATAATATTATATTTTATTTT
Found at i:2212533 original size:21 final size:21
Alignment explanation
Indices: 2212493--2212596 Score: 85
Period size: 21 Copynumber: 5.1 Consensus size: 21
2212483 TAAAATTATT
*
2212493 TTTTATTATAT-ATATT--TA
1 TTTTATTTTATAATATTAATA
*
2212511 TTTTATTTTTTAATATTAATA
1 TTTTATTTTATAATATTAATA
2212532 TTTTATTTTATAAT-TTAATCA
1 TTTTATTTTATAATATTAAT-A
* * * *
2212553 TTAATATTATAAAATATTACTA
1 TT-TTATTTTATAATATTAATA
2212575 TTTTA-TTTATAAT-TTAAATA
1 TTTTATTTTATAATATT-AATA
2212595 TT
1 TT
2212597 ATTAAGATTA
Statistics
Matches: 68, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
18 9 0.13
19 7 0.10
20 16 0.24
21 20 0.29
22 12 0.18
23 4 0.06
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTATTTTATAATATTAATA
Found at i:2212536 original size:26 final size:26
Alignment explanation
Indices: 2212488--2212560 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
2212478 ATAAATAAAA
*
2212488 TTATTTTTTATTA-T-ATATATTTATT
1 TTATTTTTTAATATTAATAT-TTTATT
2212513 TTATTTTTTAATATTAATATTTTATT
1 TTATTTTTTAATATTAATATTTTATT
**
2212539 TTATAATTTAATCATTAATATT
1 TTATTTTTTAAT-ATTAATATT
2212561 ATAAAATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 12 0.29
26 17 0.40
27 13 0.31
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (26 bp):
TTATTTTTTAATATTAATATTTTATT
Found at i:2212598 original size:36 final size:37
Alignment explanation
Indices: 2212528--2212634 Score: 98
Period size: 37 Copynumber: 2.9 Consensus size: 37
2212518 TTTTAATATT
* *
2212528 AATATTTTATTTTATAATTTAATCATT-AATATTA-TAA-
1 AATA-TTTATTTTA-ATTTTAAT-TTTAAATATTATTAAG
2212565 AATATTACTATTTT-ATTTATAA-TTTAAATATTATTAAG
1 AATATT--TATTTTAATTT-TAATTTTAAATATTATTAAG
*
2212603 ATTATTTATTTTAATTTTAATTTTAAATATTA
1 AATATTTATTTTAATTTTAATTTTAAATATTA
2212635 ATAATTTATA
Statistics
Matches: 59, Mismatches: 3, Indels: 16
0.76 0.04 0.21
Matches are distributed among these distances:
35 2 0.03
36 21 0.36
37 25 0.42
38 11 0.19
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (37 bp):
AATATTTATTTTAATTTTAATTTTAAATATTATTAAG
Found at i:2212642 original size:27 final size:26
Alignment explanation
Indices: 2212622--2212676 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
2212612 TTTAATTTTA
* *
2212622 ATTTTAAATATTAATAATTTATAATTT
1 ATTTAAAAAATTAA-AATTTATAATTT
*
2212649 ATTTAAAAAATTAAAATTTGATAGTTT
1 ATTTAAAAAATTAAAATTT-ATAATTT
2212676 A
1 A
2212677 AGTATTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (26 bp):
ATTTAAAAAATTAAAATTTATAATTT
Found at i:2212703 original size:26 final size:27
Alignment explanation
Indices: 2212664--2212714 Score: 70
Period size: 26 Copynumber: 1.9 Consensus size: 27
2212654 AAAAATTAAA
*
2212664 ATTTGATAGTTTAAGT-ATTAATATTTT
1 ATTTGATACTTTAA-TCATTAATATTTT
2212691 ATTT-ATACTTTAATCATTAATATT
1 ATTTGATACTTTAATCATTAATATT
2212715 ANNNNNNNNN
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 1 0.05
26 17 0.77
27 4 0.18
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.55
Consensus pattern (27 bp):
ATTTGATACTTTAATCATTAATATTTT
Found at i:2222907 original size:29 final size:29
Alignment explanation
Indices: 2222874--2222985 Score: 102
Period size: 32 Copynumber: 3.7 Consensus size: 29
2222864 ATAAATCGAC
*
2222874 AAATAATATAAAGACTTATTTGATTTAAA
1 AAATAATATAAAAACTTATTTGATTTAAA
2222903 AAATAAAAATATAAAAACTTATTT-AGTTTAAA
1 AAAT---AATATAAAAACTTATTTGA-TTTAAA
* * * *
2222935 ATAAAAATATAAAAACTTAATTGAATATAAT
1 A-AATAATATAAAAACTTATTTG-ATTTAAA
*
2222966 AAA-CATATAAAAACTTATTT
1 AAATAATATAAAAACTTATTT
2222986 AAATTAGTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 14
0.77 0.08 0.16
Matches are distributed among these distances:
29 19 0.28
30 18 0.26
31 6 0.09
32 24 0.35
33 2 0.03
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (29 bp):
AAATAATATAAAAACTTATTTGATTTAAA
Found at i:2222915 original size:32 final size:31
Alignment explanation
Indices: 2222878--2222985 Score: 125
Period size: 30 Copynumber: 3.5 Consensus size: 31
2222868 ATCGACAAAT
*
2222878 AATATAAAGACTTATTTGA-TTTAAAAAATAAA
1 AATATAAAAACTTATTTGAGTTT--AAAATAAA
2222910 AATATAAAAACTTATTT-AGTTTAAAATAAA
1 AATATAAAAACTTATTTGAGTTTAAAATAAA
* * *
2222940 AATATAAAAACTTAATTGA--ATATAATAAA
1 AATATAAAAACTTATTTGAGTTTAAAATAAA
*
2222969 CATATAAAAACTTATTT
1 AATATAAAAACTTATTT
2222986 AAATTAGTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
29 23 0.34
30 24 0.35
31 2 0.03
32 19 0.28
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (31 bp):
AATATAAAAACTTATTTGAGTTTAAAATAAA
Found at i:2222938 original size:30 final size:29
Alignment explanation
Indices: 2222878--2222985 Score: 126
Period size: 29 Copynumber: 3.6 Consensus size: 29
2222868 ATCGACAAAT
*
2222878 AATATAAAGACTTATTTGATTTAAAAAATAAA
1 AATATAAAAACTTATTTG-TTT--AAAATAAA
2222910 AATATAAAAACTTATTTAGTTTAAAATAAA
1 AATATAAAAACTTATTT-GTTTAAAATAAA
* ** *
2222940 AATATAAAAACTTAATTGAATATAATAAA
1 AATATAAAAACTTATTTGTTTAAAATAAA
*
2222969 CATATAAAAACTTATTT
1 AATATAAAAACTTATTT
2222986 AAATTAGTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
29 24 0.35
30 24 0.35
32 19 0.28
33 1 0.01
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (29 bp):
AATATAAAAACTTATTTGTTTAAAATAAA
Found at i:2226377 original size:72 final size:66
Alignment explanation
Indices: 2226252--2226400 Score: 167
Period size: 72 Copynumber: 2.1 Consensus size: 66
2226242 ATATAAAACG
* * *
2226252 TATTAAGAAATTAAAATAAAATATTATCTTTTAAAAAAATTAAAATAAATATATAATA-TAAGAA
1 TATTAA-AAATAAAAATAAAATATTATCTTGTAAAAAAATGAAAATAAATATATAATATTAA-AA
2226316 ATTA
64 A-TA
2226320 TATTAAAAATAAAAATAAAA-ATATATACTTGTAATAAGAAATGAAGAATAAAATATATAATATT
1 TATTAAAAATAAAAATAAAATAT-TAT-CTTGTAA-AA-AAATGAA-AAT-AAATATATAATATT
2226384 AAAAATA
60 AAAAATA
2226391 TATTTAAAAA
1 TA-TTAAAAA
2226401 ATGACATTAT
Statistics
Matches: 70, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
66 2 0.03
67 16 0.23
68 12 0.17
69 2 0.03
70 6 0.09
71 7 0.10
72 22 0.31
73 3 0.04
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (66 bp):
TATTAAAAATAAAAATAAAATATTATCTTGTAAAAAAATGAAAATAAATATATAATATTAAAAAT
A
Found at i:2228874 original size:31 final size:31
Alignment explanation
Indices: 2228846--2228903 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2228836 TTCAAAACTT
*
2228846 AAAAAA-AAAAA-AAGAGGAAGAAAGAAAAC
1 AAAAAAGAAAAAGAAGAAGAAGAAAGAAAAC
*
2228875 AAAAAAGAAAAAGAAGAAGAGGAAAGAAA
1 AAAAAAGAAAAAGAAGAAGAAGAAAGAAA
2228904 TGTTAGGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 6 0.24
30 5 0.20
31 14 0.56
ACGTcount: A:0.78, C:0.02, G:0.21, T:0.00
Consensus pattern (31 bp):
AAAAAAGAAAAAGAAGAAGAAGAAAGAAAAC
Found at i:2228888 original size:22 final size:22
Alignment explanation
Indices: 2228848--2228889 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
2228838 CAAAACTTAA
**
2228848 AAAAAAAAAAAGAGGAAGAAAG
1 AAAAAAAAAAAGAAAAAGAAAG
*
2228870 AAAACAAAAAAGAAAAAGAA
1 AAAAAAAAAAAGAAAAAGAA
2228890 GAAGAGGAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.81, C:0.02, G:0.17, T:0.00
Consensus pattern (22 bp):
AAAAAAAAAAAGAAAAAGAAAG
Found at i:2261846 original size:15 final size:15
Alignment explanation
Indices: 2261828--2261870 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
2261818 TCCATAGTTA
2261828 CCACCACCATAACTG
1 CCACCACCATAACTG
*
2261843 CCACCACCATAGCTG
1 CCACCACCATAACTG
*
2261858 CCGCCACCATAAC
1 CCACCACCATAAC
2261871 CACTATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.30, C:0.49, G:0.09, T:0.12
Consensus pattern (15 bp):
CCACCACCATAACTG
Found at i:2261846 original size:30 final size:30
Alignment explanation
Indices: 2261812--2261870 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
2261802 CATAGCCGCC
* *
2261812 GCCACCTCCATAGTTACCACCACCATAACT
1 GCCACCACCATAGCTACCACCACCATAACT
* *
2261842 GCCACCACCATAGCTGCCGCCACCATAAC
1 GCCACCACCATAGCTACCACCACCATAAC
2261871 CACTATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.46, G:0.10, T:0.15
Consensus pattern (30 bp):
GCCACCACCATAGCTACCACCACCATAACT
Found at i:2261905 original size:21 final size:21
Alignment explanation
Indices: 2261880--2261920 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
2261870 CCACTATTAA
2261880 AACCTCCACCTCCAAAGTTAT
1 AACCTCCACCTCCAAAGTTAT
2261901 AACCTCCACCTCCAAAGTTA
1 AACCTCCACCTCCAAAGTTA
2261921 CGAGGAGGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.39, G:0.05, T:0.22
Consensus pattern (21 bp):
AACCTCCACCTCCAAAGTTAT
Found at i:2265218 original size:15 final size:15
Alignment explanation
Indices: 2265183--2265220 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
2265173 TATTTCTCAA
2265183 TATATACAATTTAAAT
1 TATATA-AATTTAAAT
*
2265199 T-TATAAATTTATAT
1 TATATAAATTTAAAT
2265213 TATATAAA
1 TATATAAA
2265221 ATTTTTCTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 10 0.50
16 1 0.05
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
TATATAAATTTAAAT
Found at i:2274471 original size:20 final size:20
Alignment explanation
Indices: 2274446--2274491 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
2274436 GTGAAGGAAA
2274446 AAGAATACATAATTCTTTTC
1 AAGAATACATAATTCTTTTC
2274466 AAGAATACATAATTCTTTTC
1 AAGAATACATAATTCTTTTC
2274486 AAGAAT
1 AAGAAT
2274492 GCACTTATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (20 bp):
AAGAATACATAATTCTTTTC
Found at i:2279562 original size:13 final size:13
Alignment explanation
Indices: 2279546--2279573 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2279536 GTGAAGCTTG
2279546 AGGGTGAGAGATT
1 AGGGTGAGAGATT
2279559 AGGGTGAGAGATT
1 AGGGTGAGAGATT
2279572 AG
1 AG
2279574 AGGATCGTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.21
Consensus pattern (13 bp):
AGGGTGAGAGATT
Found at i:2283833 original size:18 final size:17
Alignment explanation
Indices: 2283799--2283830 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
2283789 TCTAAAATTA
2283799 AATTTTATAATAATTTT
1 AATTTTATAATAATTTT
2283816 AA-TTTAT-ATAATTTT
1 AATTTTATAATAATTTT
2283831 TTTTAATATG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.53
16 5 0.33
17 2 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
AATTTTATAATAATTTT
Found at i:2289453 original size:32 final size:32
Alignment explanation
Indices: 2289417--2289516 Score: 77
Period size: 32 Copynumber: 3.2 Consensus size: 32
2289407 GATGACGCAG
2289417 ATATGATACAATCTATTGTCTTACCCATTTTT
1 ATATGATACAATCTATTGTCTTACCCATTTTT
* *
2289449 ATATGA-AGCAATC-A--G-C-AACTCAATTTTGT
1 ATATGATA-CAATCTATTGTCTTAC-CCATTTT-T
* *
2289478 CCTATGGTACAATCTATTGTCTTACCCATTTTT
1 -ATATGATACAATCTATTGTCTTACCCATTTTT
*
2289511 GTATGA
1 ATATGA
2289517 AGCAATCAAC
Statistics
Matches: 50, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
27 2 0.04
28 7 0.14
29 2 0.04
30 9 0.18
31 4 0.08
32 15 0.30
33 2 0.04
34 7 0.14
35 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (32 bp):
ATATGATACAATCTATTGTCTTACCCATTTTT
Found at i:2289489 original size:62 final size:62
Alignment explanation
Indices: 2289418--2289541 Score: 221
Period size: 62 Copynumber: 2.0 Consensus size: 62
2289408 ATGACGCAGA
*
2289418 TATGATACAATCTATTGTCTTACCCATTTTTATATGAAGCAATCAGCAACTCAATTTTGTCC
1 TATGATACAATCTATTGTCTTACCCATTTTTATATGAAGCAATCAACAACTCAATTTTGTCC
* *
2289480 TATGGTACAATCTATTGTCTTACCCATTTTTGTATGAAGCAATCAACAACTCAATTTTGTCC
1 TATGATACAATCTATTGTCTTACCCATTTTTATATGAAGCAATCAACAACTCAATTTTGTCC
2289542 AATAATTTAG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (62 bp):
TATGATACAATCTATTGTCTTACCCATTTTTATATGAAGCAATCAACAACTCAATTTTGTCC
Found at i:2294149 original size:38 final size:38
Alignment explanation
Indices: 2294094--2294173 Score: 144
Period size: 38 Copynumber: 2.1 Consensus size: 38
2294084 ATCGTAAGGC
*
2294094 TTTT-GGCAATAATATTGAATTGTACCTCTCAATTATG
1 TTTTAGGCAATAATATTGAATTGTAACTCTCAATTATG
2294131 TTTTAGGCAATAATATTGAATTGTAACTCTCAATTATG
1 TTTTAGGCAATAATATTGAATTGTAACTCTCAATTATG
2294169 TTTTA
1 TTTTA
2294174 AGTTGTCCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 4 0.10
38 37 0.90
ACGTcount: A:0.31, C:0.11, G:0.12, T:0.45
Consensus pattern (38 bp):
TTTTAGGCAATAATATTGAATTGTAACTCTCAATTATG
Found at i:2296637 original size:23 final size:23
Alignment explanation
Indices: 2296610--2296665 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2296600 ATGTATCATC
2296610 AAACATAACAATCACATAACACA
1 AAACATAACAATCACATAACACA
* * * * *
2296633 TAACATATCATTCACATTACATA
1 AAACATAACAATCACATAACACA
2296656 AAACATAACA
1 AAACATAACA
2296666 TCATATCTAC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.21
Consensus pattern (23 bp):
AAACATAACAATCACATAACACA
Found at i:2297955 original size:28 final size:29
Alignment explanation
Indices: 2297879--2297975 Score: 76
Period size: 28 Copynumber: 3.3 Consensus size: 29
2297869 TTTATTCTTA
* * *
2297879 TTTTCAATTTGGTCATCAAACTTTTT-TA-
1 TTTTCAATTTGATCCTCTAA-TTTTTCTAC
* *
2297907 TTTTGAATTTGATCTTCTAATTTTTCTAC
1 TTTTCAATTTGATCCTCTAATTTTTCTAC
*
2297936 TTTT-AATTTGATCC-CTTAATCTTTTCATGC
1 TTTTCAATTTGATCCTC-TAAT-TTTTC-TAC
2297966 TTTTCAATTT
1 TTTTCAATTT
2297976 AGTCCCTCTT
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
27 6 0.11
28 31 0.54
29 9 0.16
30 6 0.11
31 5 0.09
ACGTcount: A:0.22, C:0.15, G:0.06, T:0.57
Consensus pattern (29 bp):
TTTTCAATTTGATCCTCTAATTTTTCTAC
Found at i:2308757 original size:53 final size:53
Alignment explanation
Indices: 2308674--2308781 Score: 155
Period size: 53 Copynumber: 2.0 Consensus size: 53
2308664 GAGTGCCCAC
* * *
2308674 ATGCATGTAAGTGTTTTTTTTTTTATATAGTCAAGTTGATTTAGTGATCTAAA
1 ATGCATGTAAGTGTTTTTTTTTTTACATAGTCAAATTGATTTAGTAATCTAAA
* *
2308727 ATGCATGTATGTGTTTTATTTTTTT-CATAGTCAAATTGATTTAGTAATCTGAA
1 ATGCATGTAAGTGTTTT-TTTTTTTACATAGTCAAATTGATTTAGTAATCTAAA
2308780 AT
1 AT
2308782 TATATAATCA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
53 42 0.86
54 7 0.14
ACGTcount: A:0.29, C:0.06, G:0.16, T:0.49
Consensus pattern (53 bp):
ATGCATGTAAGTGTTTTTTTTTTTACATAGTCAAATTGATTTAGTAATCTAAA
Done.