Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006710.1 Hibiscus syriacus cultivar Beakdansim tig00016725_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: 2941931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1536670 original size:21 final size:23
Alignment explanation
Indices: 1536622--1536672 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
1536612 GATTCCCTGT
1536622 GGGGGGAATCGGTTCCCCTTCAA
1 GGGGGGAATCGGTTCCCCTTCAA
*
1536645 AGGGGGAATCGGTT-CCC-TCAA
1 GGGGGGAATCGGTTCCCCTTCAA
1536666 GGGGGGA
1 GGGGGGA
1536673 TCGATTCACT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 10 0.38
22 3 0.12
23 13 0.50
ACGTcount: A:0.20, C:0.22, G:0.41, T:0.18
Consensus pattern (23 bp):
GGGGGGAATCGGTTCCCCTTCAA
Found at i:1545318 original size:14 final size:14
Alignment explanation
Indices: 1545295--1545335 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
1545285 ATATATACAT
*
1545295 TATTATATATA-TA
1 TATTATAAATATTA
1545308 TA-TATAAATATTA
1 TATTATAAATATTA
1545321 TATTATAAATATTA
1 TATTATAAATATTA
1545335 T
1 T
1545336 TATTTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 7 0.28
13 6 0.24
14 12 0.48
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATTATAAATATTA
Found at i:1546655 original size:27 final size:28
Alignment explanation
Indices: 1546625--1546690 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 28
1546615 TCATATAGTT
* *
1546625 TTAATATTAAATATTATAGTAG-GATTA
1 TTAATATTAAATATTAAAGTAGTAATTA
* *
1546652 TTAATATT-GATATTAAATTAGTAATTA
1 TTAATATTAAATATTAAAGTAGTAATTA
*
1546679 TTTATATTAAAT
1 TTAATATTAAAT
1546691 TAGTAGTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 10 0.32
27 19 0.61
28 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (28 bp):
TTAATATTAAATATTAAAGTAGTAATTA
Found at i:1546685 original size:21 final size:20
Alignment explanation
Indices: 1546648--1546695 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
1546638 TTATAGTAGG
*
1546648 ATTATTAATATTGATATTAA
1 ATTAGTAATATTGATATTAA
*
1546668 ATTAGTAATTATTTATATTAA
1 ATTAGTAA-TATTGATATTAA
1546689 ATTAGTA
1 ATTAGTA
1546696 GTAAATTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (20 bp):
ATTAGTAATATTGATATTAA
Found at i:1546708 original size:21 final size:21
Alignment explanation
Indices: 1546663--1546709 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
1546653 TAATATTGAT
* * *
1546663 ATTAAATTAGTAATTATTTAT
1 ATTAAATTAGTAATAAATTAA
*
1546684 ATTAAATTAGTAGTAAATTAA
1 ATTAAATTAGTAATAAATTAA
1546705 ATTAA
1 ATTAA
1546710 TTACAAGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (21 bp):
ATTAAATTAGTAATAAATTAA
Found at i:1554040 original size:51 final size:47
Alignment explanation
Indices: 1553979--1554095 Score: 119
Period size: 51 Copynumber: 2.4 Consensus size: 47
1553969 ATTTTTGGGT
* * * *
1553979 TTCACGGAAGAGTAGTGAAACAAA-TGTTGTTCAACTTATACAAATTCAGCC
1 TTCACAGAAGAGTAGTGAAACAAATTGTT-TGCAACTCAT-C---CTCAGCC
* * *
1554030 TTCACAGAAGAGTAGCGAAGCAAATTGTTTGCAAGTCATCCTCAGCC
1 TTCACAGAAGAGTAGTGAAACAAATTGTTTGCAACTCATCCTCAGCC
1554077 TTCACAGAAGAGTAGTGAA
1 TTCACAGAAGAGTAGTGAA
1554096 GCAAGAGCAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
47 24 0.42
50 1 0.02
51 28 0.49
52 4 0.07
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.25
Consensus pattern (47 bp):
TTCACAGAAGAGTAGTGAAACAAATTGTTTGCAACTCATCCTCAGCC
Found at i:1565450 original size:2 final size:2
Alignment explanation
Indices: 1565445--1565489 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1565435 TATATCCATC
1565445 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1565487 TA T
1 TA T
1565490 TAAAAAAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1578828 original size:14 final size:16
Alignment explanation
Indices: 1578811--1578854 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 16
1578801 TTTAGACATT
1578811 TTATTTTATTT-TTC-
1 TTATTTTATTTATTCA
1578825 TTATTCTTATTTATTCA
1 TTATT-TTATTTATTCA
1578842 TTATTTT-TTTATT
1 TTATTTTATTTATT
1578855 TTTAAGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.19
15 12 0.44
16 5 0.19
17 5 0.19
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (16 bp):
TTATTTTATTTATTCA
Found at i:1584496 original size:57 final size:55
Alignment explanation
Indices: 1584434--1584613 Score: 132
Period size: 57 Copynumber: 3.2 Consensus size: 55
1584424 TCTCAAAATA
* * *
1584434 TTTTATAAACTACAATAAAGCCCAAACTTTTCATAAATTATATTACTAACCTAAA-CT
1 TTTTATAAA-TACAATAAAGCCCAAACTTTTCATAAATTACAATAAT-ACC-AAATCT
* * * *
1584491 TTTTATAAATCATAATAAATG-CCAAACATTCCATAAATTACAATAATACCAAATTT
1 TTTTATAAAT-ACAATAAA-GCCCAAACTTTTCATAAATTACAATAATACCAAATCT
* * *** * *
1584547 TTTTACAAATTACAATAGAAACCCAAACTTTTTGCAAATTATAATAAAGACCAAA-CT
1 TTTTATAAA-TACAATA-AAGCCCAAACTTTTCATAAATTACAAT-AATACCAAATCT
*
1584604 TTTTACAAAT
1 TTTTATAAAT
1584614 TACAGTAGAA
Statistics
Matches: 98, Mismatches: 18, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
55 3 0.03
56 19 0.19
57 67 0.68
58 9 0.09
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (55 bp):
TTTTATAAATACAATAAAGCCCAAACTTTTCATAAATTACAATAATACCAAATCT
Found at i:1584556 original size:28 final size:27
Alignment explanation
Indices: 1584411--1584633 Score: 131
Period size: 28 Copynumber: 7.8 Consensus size: 27
1584401 CACAATATTA
* * *
1584411 AAATTACAATAAATCTCAAAATATTTTAT
1 AAATTACAATAAAAC-CAAACT-TTTTAC
* * * *
1584440 AAACTACAATAAAGCCCAAACTTTTCAT
1 AAATTACAATAAA-ACCAAACTTTTTAC
* * * *
1584468 AAATTATATTACTAACCTAAACTTTTTAT
1 AAATTACAATA-AAACC-AAACTTTTTAC
* * * * ** *
1584497 AAATCATAATAAATGCCAAACATTCCAT
1 AAATTACAATAAA-ACCAAACTTTTTAC
* *
1584525 AAATTACAATAATACCAAATTTTTTTAC
1 AAATTACAATAAAACCAAA-CTTTTTAC
*
1584553 AAATTACAATAGAAACCCAAACTTTTTGC
1 AAATTACAATA-AAA-CCAAACTTTTTAC
*
1584582 AAATTATAATAAAGACCAAACTTTTTAC
1 AAATTACAATAAA-ACCAAACTTTTTAC
*
1584610 AAATTACAGTAGAAACTCAAACTT
1 AAATTACAATA-AAAC-CAAACTT
1584634 CTCAAAATTA
Statistics
Matches: 151, Mismatches: 33, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
27 5 0.03
28 73 0.48
29 67 0.44
30 6 0.04
ACGTcount: A:0.48, C:0.17, G:0.03, T:0.32
Consensus pattern (27 bp):
AAATTACAATAAAACCAAACTTTTTAC
Found at i:1584732 original size:29 final size:29
Alignment explanation
Indices: 1584658--1584732 Score: 73
Period size: 29 Copynumber: 2.6 Consensus size: 29
1584648 TAAATACCCC
*
1584658 TTCATACATGAAGTATACCAAATTCTCAAT
1 TTCATACATGAAGTTTA-CAAATTCTCAAT
* *
1584688 TTCTTACAT-AATGTTTA-AAATTTCTCGAT
1 TTCATACATGAA-GTTTACAAA-TTCTCAAT
*
1584717 TTCATACATGACGTTT
1 TTCATACATGAAGTTT
1584733 TTTTTCCATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 3 0.08
29 21 0.57
30 13 0.35
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.41
Consensus pattern (29 bp):
TTCATACATGAAGTTTACAAATTCTCAAT
Found at i:1584994 original size:12 final size:12
Alignment explanation
Indices: 1584977--1585020 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
1584967 ACAAAAAAAA
1584977 TCACTAATTTTT
1 TCACTAATTTTT
1584989 TCACTAATTTTT
1 TCACTAATTTTT
* **
1585001 TAAAAATATTTTT
1 TCACTA-ATTTTT
1585014 TCACTAA
1 TCACTAA
1585021 AATTTAGTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
12 16 0.64
13 9 0.36
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (12 bp):
TCACTAATTTTT
Found at i:1585232 original size:24 final size:23
Alignment explanation
Indices: 1585175--1585220 Score: 83
Period size: 24 Copynumber: 2.0 Consensus size: 23
1585165 TTATGTTCGA
1585175 TTAAACCGATTAAAATATTTTTG
1 TTAAACCGATTAAAATATTTTTG
1585198 TTAAAACCGATTAAAATATTTTT
1 TT-AAACCGATTAAAATATTTTT
1585221 TGATTAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (23 bp):
TTAAACCGATTAAAATATTTTTG
Found at i:1585399 original size:18 final size:18
Alignment explanation
Indices: 1585376--1585432 Score: 78
Period size: 18 Copynumber: 3.0 Consensus size: 18
1585366 TTAGTGAAAC
1585376 AATTTAGTGAAAATTTTA
1 AATTTAGTGAAAATTTTA
*
1585394 AATTTAGTGAATATTTTAA
1 AATTTAGTGAAAATTTT-A
1585413 AATTTTCAGTGAAAATTTTA
1 AA-TTT-AGTGAAAATTTTA
1585433 TTTTAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 16 0.47
19 3 0.09
20 4 0.12
21 11 0.32
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.46
Consensus pattern (18 bp):
AATTTAGTGAAAATTTTA
Found at i:1586795 original size:3 final size:3
Alignment explanation
Indices: 1586787--1586834 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
1586777 TCTACAAAAA
1586787 TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1586833 TA
1 TA
1586835 ACAACAATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1586811 original size:20 final size:20
Alignment explanation
Indices: 1586786--1586834 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1586776 GTCTACAAAA
1586786 ATATTATTATTATTATTATT
1 ATATTATTATTATTATTATT
1586806 ATATTATTATTATTATTATT
1 ATATTATTATTATTATTATT
*
1586826 ATTTTATTA
1 ATATTATTA
1586835 ACAACAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATATTATTATTATTATTATT
Found at i:1586898 original size:13 final size:13
Alignment explanation
Indices: 1586866--1586899 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1586856 GACTTCACCG
1586866 AAGCCCA-ATTAC
1 AAGCCCAGATTAC
1586878 AAGACCCAGATTAC
1 AAG-CCCAGATTAC
1586892 AAGCCCAG
1 AAGCCCAG
1586900 CAACACAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 9 0.45
14 8 0.40
ACGTcount: A:0.41, C:0.32, G:0.15, T:0.12
Consensus pattern (13 bp):
AAGCCCAGATTAC
Found at i:1588264 original size:30 final size:30
Alignment explanation
Indices: 1588222--1588361 Score: 172
Period size: 30 Copynumber: 4.6 Consensus size: 30
1588212 GAAATTACTG
* * *
1588222 TTTAGCCCTTTAAGTTTTTATTTTTTCTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
* * * *
1588252 TTAAGTCCTTTAACTTTCTATATTTGTTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
*
1588282 TTTAGTCCTTTAAGTTTATATTTTTGCTAT
1 TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
* *
1588312 TGTTAGTCCTTTAACTTTCTATTTTAGCTAT
1 T-TTAGTCCTTTAAGTTTCTATTTTTGCTAT
*
1588343 TTTAGTACTTTAAGTTTCT
1 TTTAGTCCTTTAAGTTTCT
1588362 GTTATTTTTA
Statistics
Matches: 92, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
30 65 0.71
31 27 0.29
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.59
Consensus pattern (30 bp):
TTTAGTCCTTTAAGTTTCTATTTTTGCTAT
Found at i:1588346 original size:61 final size:60
Alignment explanation
Indices: 1588222--1588359 Score: 197
Period size: 61 Copynumber: 2.3 Consensus size: 60
1588212 GAAATTACTG
* * * *
1588222 TTTAGCCCTTTAAGTTTTTATTTTTTCTATTTAAGTCCTTTAACTTTCTATATTTGTTAT
1 TTTAGTCCTTTAAGTTTATATTTTTGCTATTTAAGTCCTTTAACTTTCTATATTTGCTAT
*
1588282 TTTAGTCCTTTAAGTTTATATTTTTGCTATTGTTAGTCCTTTAACTTTCTAT-TTTAGCTAT
1 TTTAGTCCTTTAAGTTTATATTTTTGCTATT-TAAGTCCTTTAACTTTCTATATTT-GCTAT
*
1588343 TTTAGTACTTTAAGTTT
1 TTTAGTCCTTTAAGTTT
1588360 CTGTTATTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
60 31 0.44
61 39 0.56
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.59
Consensus pattern (60 bp):
TTTAGTCCTTTAAGTTTATATTTTTGCTATTTAAGTCCTTTAACTTTCTATATTTGCTAT
Found at i:1589162 original size:16 final size:15
Alignment explanation
Indices: 1589136--1589172 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 15
1589126 AGACTAGTTT
1589136 TTTTGTCTTAAAATTG
1 TTTT-TCTTAAAATTG
1589152 ATTTTTCTTAAAATTG
1 -TTTTTCTTAAAATTG
1589168 TTTTT
1 TTTTT
1589173 AGAAGACGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 5 0.25
16 11 0.55
17 4 0.20
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TTTTTCTTAAAATTG
Found at i:1592097 original size:7 final size:7
Alignment explanation
Indices: 1592071--1592110 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
1592061 AAATCAAAAT
*
1592071 AAAGAAC
1 AAAGAGC
1592078 AAAGAGC
1 AAAGAGC
1592085 AAAGAGC
1 AAAGAGC
1592092 AAAGAG-
1 AAAGAGC
1592098 AAAGAAGC
1 AAAG-AGC
1592106 AAAGA
1 AAAGA
1592111 AAAACCAAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
6 4 0.13
7 22 0.73
8 4 0.13
ACGTcount: A:0.65, C:0.10, G:0.25, T:0.00
Consensus pattern (7 bp):
AAAGAGC
Found at i:1592122 original size:31 final size:30
Alignment explanation
Indices: 1592086--1592143 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
1592076 ACAAAGAGCA
*
1592086 AAGAGCAAAGAGAAAGAAGCAAAGAAAAACC
1 AAGAGCAAAGAGAAA-AAACAAAGAAAAACC
1592117 AAGAGCAAAGAGAAAAAACAAAGAAAA
1 AAGAGCAAAGAGAAAAAACAAAGAAAA
1592144 GAAAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 11 0.42
31 15 0.58
ACGTcount: A:0.69, C:0.10, G:0.21, T:0.00
Consensus pattern (30 bp):
AAGAGCAAAGAGAAAAAACAAAGAAAAACC
Found at i:1592132 original size:19 final size:16
Alignment explanation
Indices: 1592106--1592167 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 16
1592096 AGAAAGAAGC
*
1592106 AAAGAAAAACCAAGAGCA
1 AAAGAAAAAACAA-AG-A
1592124 AAGAGAAAAAACAAAGA
1 AA-AGAAAAAACAAAGA
* *
1592141 AAAGAAAAAAGAAAAA
1 AAAGAAAAAACAAAGA
1592157 GAAAGAAAAAA
1 -AAAGAAAAAA
1592168 GAAAAAGAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
16 12 0.31
17 13 0.33
18 4 0.10
19 10 0.26
ACGTcount: A:0.77, C:0.06, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAACAAAGA
Found at i:1592143 original size:11 final size:11
Alignment explanation
Indices: 1592127--1592179 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
1592117 AAGAGCAAAG
*
1592127 AGAAAAAACAA
1 AGAAAAAAAAA
1592138 AGAAAAGAAAAA
1 AGAAAA-AAAAA
1592150 AGAAAAAGAAAGA
1 AGAAAAA-AAA-A
*
1592163 A-AAAAGAAAA
1 AGAAAAAAAAA
1592173 AGAAAAA
1 AGAAAAA
1592180 GCGAAGAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 2 0.06
11 14 0.40
12 17 0.49
13 2 0.06
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:1592161 original size:17 final size:17
Alignment explanation
Indices: 1592127--1592177 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
1592117 AAGAGCAAAG
* *
1592127 AGAAAAAACAAAGA-AA
1 AGAAAAAAGAAAAAGAA
1592143 AGAAAAAAGAAAAAGAA
1 AGAAAAAAGAAAAAGAA
1592160 AGAAAAAAGAAAAAGAA
1 AGAAAAAAGAAAAAGAA
1592177 A
1 A
1592178 AAGCGAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 12 0.38
17 20 0.62
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (17 bp):
AGAAAAAAGAAAAAGAA
Found at i:1592166 original size:23 final size:23
Alignment explanation
Indices: 1592130--1592191 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
1592120 AGCAAAGAGA
* *
1592130 AAAAACAAAGAAAAGA-AAAAAG
1 AAAAAGAAAGAAAAAAGAAAAAG
1592152 AAAAAGAAAGAAAAAAGAAAAAG
1 AAAAAGAAAGAAAAAAGAAAAAG
*
1592175 AAAAAGCGAAGAAAAAA
1 AAAAAG-AAAGAAAAAA
1592192 AGAGACAATA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 14 0.40
23 12 0.34
24 9 0.26
ACGTcount: A:0.81, C:0.03, G:0.16, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAGAAAAAAGAAAAAG
Found at i:1592167 original size:24 final size:24
Alignment explanation
Indices: 1592127--1592191 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
1592117 AAGAGCAAAG
* *
1592127 AGAAAAAACAAAGAAAAGA-AAAA
1 AGAAAAAGCAAAGAAAAAAGAAAA
1592150 AGAAAAAG-AAAGAAAAAAGAAAA
1 AGAAAAAGCAAAGAAAAAAGAAAA
*
1592173 AGAAAAAGCGAAGAAAAAA
1 AGAAAAAGCAAAGAAAAAA
1592192 AGAGACAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
22 9 0.24
23 19 0.51
24 9 0.24
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (24 bp):
AGAAAAAGCAAAGAAAAAAGAAAA
Found at i:1593576 original size:30 final size:29
Alignment explanation
Indices: 1593532--1593620 Score: 108
Period size: 30 Copynumber: 3.0 Consensus size: 29
1593522 CTTTTGAAGG
*
1593532 AAAATCTTTGAGTATGTTTCTCTTGAAAT
1 AAAATCTTTGAGTATGTTTCTCTTGAAAC
* *
1593561 AAAAGTCTTTTAGTATGTTTCTCTTAAAAC
1 AAAA-TCTTTGAGTATGTTTCTCTTGAAAC
*
1593591 AAACATCTTTGAG-ATTGTTTCCCTTGAAAC
1 AAA-ATCTTTGAGTA-TGTTTCTCTTGAAAC
1593621 GAATTTCGTC
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 5 0.10
30 45 0.88
31 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (29 bp):
AAAATCTTTGAGTATGTTTCTCTTGAAAC
Found at i:1593757 original size:15 final size:16
Alignment explanation
Indices: 1593727--1593758 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1593717 TCACGTAGGA
1593727 ACCGTGTCATCCCCTG
1 ACCGTGTCATCCCCTG
1593743 ACCGTGTCA-CCCCTG
1 ACCGTGTCATCCCCTG
1593758 A
1 A
1593759 TAACCAGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.16, C:0.44, G:0.19, T:0.22
Consensus pattern (16 bp):
ACCGTGTCATCCCCTG
Found at i:1593999 original size:130 final size:129
Alignment explanation
Indices: 1593747--1594148 Score: 344
Period size: 130 Copynumber: 3.1 Consensus size: 129
1593737 CCCCTGACCG
* *
1593747 TGTCACCCCTGATAACCAGCCATCCTCATCACATAGGAACCGTGTTATCATCCCTAAAGATGGCC
1 TGTCACCCCTGATAACCAGCCATCCTCATCACATAGGAACCATGTTATCATCCCTAAAGATGGAC
* * * *
1593812 AGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCTAACCAGTCCTCCTAATGACGTAGGAGCCA
66 AGCCGTCCTCATCACG-AGGAACCATGTCATCACCTAACCAGACCTCCTAATCACGTAGGAGCCA
1593877 TGTCACCCCTGATAACCAGCCATCCTCATCACATAGGAACCATGTTATCATCCC-AAGAGATGGA
1 TGTCACCCCTGATAACCAGCCATCCTCATCACATAGGAACCATGTTATCATCCCTAA-AGATGGA
* ** ** * * * *
1593941 CTGTTGTGTTCATTGCAC-AGGAACCATGTCATTCACC-GACTAGACCTCTTCATCACGTAGGAG
65 CAGCCGTCCTCA-T-CACGAGGAACCATGTCA-TCACCTAACCAGACCTCCTAATCACGTAGGAG
* *
1594004 TCG
127 CCA
* * * ** * * * *
1594007 TGTCACCCCTAGATAACCAGTCGTCCTCTTTGCGTAGGAACCGTGTTATCACCCCTCCTAAATAT
1 TGTCACCCCT-GATAACCAGCCATCCTCATCACATAGGAACCATGTTATCA--TC-CCTAAAGAT
* *** * * * * * * *
1594072 GGCCAAAAGTCTTCATCACGTATGAGCCATGTCATTCA-CTGACCAGATCTCCTCATCACGTACG
62 GGACAGCCGTCCTCATCACG-AGGAACCATGTCA-TCACCTAACCAGACCTCCTAATCACGTAGG
1594136 AGCCA
125 AGCCA
1594141 TGTCACCC
1 TGTCACCC
1594149 TTAGACGACC
Statistics
Matches: 220, Mismatches: 40, Indels: 20
0.79 0.14 0.07
Matches are distributed among these distances:
129 2 0.01
130 109 0.50
131 38 0.17
132 6 0.03
133 3 0.01
134 60 0.27
135 2 0.01
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.24
Consensus pattern (129 bp):
TGTCACCCCTGATAACCAGCCATCCTCATCACATAGGAACCATGTTATCATCCCTAAAGATGGAC
AGCCGTCCTCATCACGAGGAACCATGTCATCACCTAACCAGACCTCCTAATCACGTAGGAGCCA
Found at i:1594173 original size:43 final size:40
Alignment explanation
Indices: 1594081--1594187 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 40
1594071 TGGCCAAAAG
*
1594081 TCTTCATCACGTATGAGCCATGTCATTCACTGACCAGATC
1 TCTTCATCACGTATGAGCCATGTCATTCACTGACCAGACC
* * *
1594121 TCCTCATCACGTACGAGCCATGTCACCCTTAGAC-GACCAGACC
1 TCTTCATCACGTATGAGCCATGTCA---TT-CACTGACCAGACC
*
1594164 TCTTCATCACGTATGAGCCGTGTC
1 TCTTCATCACGTATGAGCCATGTC
1594188 GTCCCCCAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
40 23 0.41
43 31 0.55
44 2 0.04
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (40 bp):
TCTTCATCACGTATGAGCCATGTCATTCACTGACCAGACC
Found at i:1594352 original size:3 final size:3
Alignment explanation
Indices: 1594344--1594390 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
1594334 TATACAAAAA
* *
1594344 TAT TAT TAT TA- TAG TAT TAT TAT TA- TGT TAT TAT TAT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1594389 TA
1 TA
1594391 ACAACAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
2 5 0.13
3 33 0.87
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1594363 original size:14 final size:14
Alignment explanation
Indices: 1594344--1594390 Score: 69
Period size: 14 Copynumber: 3.4 Consensus size: 14
1594334 TATACAAAAA
1594344 TATTATTATTATAG-
1 TATTATTATTAT-GT
1594358 TATTATTATTATGT
1 TATTATTATTATGT
*
1594372 TATTATTATTATTT
1 TATTATTATTATGT
1594386 TATTA
1 TATTA
1594391 ACAACAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 1 0.03
14 30 0.97
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (14 bp):
TATTATTATTATGT
Found at i:1595785 original size:30 final size:29
Alignment explanation
Indices: 1595751--1595825 Score: 123
Period size: 30 Copynumber: 2.6 Consensus size: 29
1595741 TTGTTTTTAC
1595751 TATTTAAGTCCTTTAACTTTCTATTTTTGT
1 TATTTAAGTCCTTTAACTTTCTATTTTT-T
* *
1595781 TATTTTAGTCCTTTAAGTTTCTATTTTTT
1 TATTTAAGTCCTTTAACTTTCTATTTTTT
1595810 TATTTAAGTCCTTTAA
1 TATTTAAGTCCTTTAA
1595826 ATTTTAGAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.21, C:0.12, G:0.07, T:0.60
Consensus pattern (29 bp):
TATTTAAGTCCTTTAACTTTCTATTTTTT
Found at i:1596608 original size:18 final size:18
Alignment explanation
Indices: 1596570--1596607 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1596560 ACCGCAGACC
*
1596570 AAATTATTTTGTCTTAAA
1 AAATGATTTTGTCTTAAA
1596588 AAATGATTTT-TCTTAAA
1 AAATGATTTTGTCTTAAA
1596605 AAA
1 AAA
1596608 AATTTAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (18 bp):
AAATGATTTTGTCTTAAA
Found at i:1596928 original size:30 final size:31
Alignment explanation
Indices: 1596892--1596974 Score: 107
Period size: 31 Copynumber: 2.7 Consensus size: 31
1596882 ATCGCTGAAT
*
1596892 TTTAGATAAAATATTAATTTGA-CTC-TAAAC
1 TTTAGATAAAATATTAATTTAATC-CGTAAAC
*
1596922 TTTAGATAAAATATTAATTTAATCCGTGAAC
1 TTTAGATAAAATATTAATTTAATCCGTAAAC
* *
1596953 TTCATATAAAATATTAATTTAA
1 TTTAGATAAAATATTAATTTAA
1596975 CATCTGAATC
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
30 22 0.47
31 25 0.53
ACGTcount: A:0.45, C:0.08, G:0.06, T:0.41
Consensus pattern (31 bp):
TTTAGATAAAATATTAATTTAATCCGTAAAC
Found at i:1597072 original size:26 final size:26
Alignment explanation
Indices: 1597021--1597078 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1597011 CGATCATCAT
*
1597021 CGTTTTTGCCGATCATTAGTAGTTGA
1 CGTTTTTGCCGATCATTACTAGTTGA
*
1597047 CGTTTTTGTCGATCATTATCTA-TTGA
1 CGTTTTTGCCGATCATTA-CTAGTTGA
*
1597073 CATTTT
1 CGTTTT
1597079 CGGTCACCGT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 26 0.93
27 2 0.07
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (26 bp):
CGTTTTTGCCGATCATTACTAGTTGA
Found at i:1617141 original size:20 final size:20
Alignment explanation
Indices: 1617077--1617146 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
1617067 ACAAATGTTT
* *
1617077 TGTGAATAGTACT-TTAATG
1 TGTGAATAGTACTAATACTG
*
1617096 TGTGAATAGTACTGATACTG
1 TGTGAATAGTACTAATACTG
* *
1617116 TATGAATAGTA-TCAATATTG
1 TGTGAATAGTACT-AATACTG
*
1617136 TGTGAACAGTA
1 TGTGAATAGTA
1617147 ATGAATAGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
19 14 0.33
20 28 0.67
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.37
Consensus pattern (20 bp):
TGTGAATAGTACTAATACTG
Found at i:1618936 original size:83 final size:83
Alignment explanation
Indices: 1618828--1619046 Score: 251
Period size: 83 Copynumber: 2.6 Consensus size: 83
1618818 AATAGAGTTG
* * * * *
1618828 TTTATAGTGGTATTTTTCCAACAAATGCCG-TAATAGAGTATTAATATAGCGGTATCTATCAAAT
1 TTTATAGTGGTATTTATCTAACAAATGCTGCT-ATAGAGTAGTAATTTAGCGGTATCTATCAAAT
* *
1618892 AAATACCATAACAGGGTTA
65 AAACACCACAACAGGGTTA
* * * * ** *
1618911 TTTATAGTGGTGTTTCTCTAACAAATGATGCTATAGAGTAGTAATTTAGTGGCGTTTATCAAATA
1 TTTATAGTGGTATTTATCTAACAAATGCTGCTATAGAGTAGTAATTTAGCGGTATCTATCAAATA
* * *
1618976 AACACCGCAATAGGGTTG
66 AACACCACAACAGGGTTA
* *
1618994 TTTATAGTGGCATTTATCTAACAAACGCTGCTATAGAGTAGTAATTTAGCGGT
1 TTTATAGTGGTATTTATCTAACAAATGCTGCTATAGAGTAGTAATTTAGCGGT
1619047 GCTTTTCCTA
Statistics
Matches: 112, Mismatches: 23, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
83 111 0.99
84 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (83 bp):
TTTATAGTGGTATTTATCTAACAAATGCTGCTATAGAGTAGTAATTTAGCGGTATCTATCAAATA
AACACCACAACAGGGTTA
Found at i:1619081 original size:83 final size:83
Alignment explanation
Indices: 1618860--1619086 Score: 242
Period size: 83 Copynumber: 2.7 Consensus size: 83
1618850 AAATGCCGTA
* * ** * * **
1618860 ATAGAGTATTAATATAGCGGTATCTATCAAATAAATACCATAACAGGGTTATTTATAGTGGTGTT
1 ATAGAGTAGTAATTTAGCGGCGTTTATCAAATAAATACCATAATAGGGTTATTTATAGTGGCATT
* *
1618925 TCTCTAACAAATGATGCT
66 TATCTAACAAACGATGCT
* * ** *
1618943 ATAGAGTAGTAATTTAGTGGCGTTTATCAAATAAACACCGCAATAGGGTTGTTTATAGTGGCATT
1 ATAGAGTAGTAATTTAGCGGCGTTTATCAAATAAATACCATAATAGGGTTATTTATAGTGGCATT
*
1619008 TATCTAACAAACGCTGCT
66 TATCTAACAAACGATGCT
* * * *
1619026 ATAGAGTAGTAATTTAGCGGTGCTTT-TCCTAA-AAATGCCATAATATGGTTATTTATAGTGG
1 ATAGAGTAGTAATTTAGCGGCG-TTTAT-CAAATAAATACCATAATAGGGTTATTTATAGTGG
1619087 TATTATTGGA
Statistics
Matches: 117, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
83 111 0.95
84 6 0.05
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.35
Consensus pattern (83 bp):
ATAGAGTAGTAATTTAGCGGCGTTTATCAAATAAATACCATAATAGGGTTATTTATAGTGGCATT
TATCTAACAAACGATGCT
Found at i:1626419 original size:21 final size:22
Alignment explanation
Indices: 1626390--1626432 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
1626380 CCCTATCTTA
1626390 TATTATATCAT-TCATACATTT
1 TATTATATCATATCATACATTT
*
1626411 TATTCTATCATAATCATACATT
1 TATTATATCAT-ATCATACATT
1626433 CACATGTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (22 bp):
TATTATATCATATCATACATTT
Found at i:1631263 original size:13 final size:13
Alignment explanation
Indices: 1631245--1631270 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1631235 GGCTATTGTC
1631245 TATTGTTTATGGT
1 TATTGTTTATGGT
1631258 TATTGTTTATGGT
1 TATTGTTTATGGT
1631271 ATATGGTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (13 bp):
TATTGTTTATGGT
Found at i:1631263 original size:20 final size:20
Alignment explanation
Indices: 1631238--1631280 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1631228 TATATTAGGC
* *
1631238 TATTGTCTATTGTTTATGGT
1 TATTGTCTATGGTATATGGT
*
1631258 TATTGTTTATGGTATATGGT
1 TATTGTCTATGGTATATGGT
1631278 TAT
1 TAT
1631281 AGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.02, G:0.21, T:0.58
Consensus pattern (20 bp):
TATTGTCTATGGTATATGGT
Found at i:1638610 original size:20 final size:20
Alignment explanation
Indices: 1638573--1638615 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1638563 TATATTGGGC
* *
1638573 TATTGTCTATTGTTTATGAT
1 TATTGTCTATGGTATATGAT
*
1638593 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATATGAT
1638613 TAT
1 TAT
1638616 GGAATAATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.19, T:0.56
Consensus pattern (20 bp):
TATTGTCTATGGTATATGAT
Found at i:1645277 original size:3 final size:3
Alignment explanation
Indices: 1645271--1645297 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1645261 AAGAAACGTG
1645271 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1645298 AAATACCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:1691701 original size:24 final size:24
Alignment explanation
Indices: 1691634--1691701 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
1691624 GACATGTCAT
* *
1691634 TTGACGTTCCAACAGTTATGCCAC
1 TTGAAGTTCCAACAGTTGTGCCAC
* * *
1691658 TTGAAGTTCAAAGAGATGTGCCAC
1 TTGAAGTTCCAACAGTTGTGCCAC
1691682 TTGAAGTTCC-ACAAGTTGTG
1 TTGAAGTTCCAAC-AGTTGTG
1691702 ATCCTTGAGG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.28, C:0.21, G:0.22, T:0.29
Consensus pattern (24 bp):
TTGAAGTTCCAACAGTTGTGCCAC
Found at i:1694186 original size:13 final size:14
Alignment explanation
Indices: 1694168--1694200 Score: 59
Period size: 13 Copynumber: 2.4 Consensus size: 14
1694158 TGCTATTATC
1694168 TATTGTTTATGGT-
1 TATTGTTTATGGTA
1694181 TATTGTTTATGGTA
1 TATTGTTTATGGTA
1694195 TATTGT
1 TATTGT
1694201 CATAGAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.61
Consensus pattern (14 bp):
TATTGTTTATGGTA
Found at i:1713397 original size:2 final size:2
Alignment explanation
Indices: 1713390--1713428 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1713380 ATCACCAACT
1713390 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
1713429 CCGCTACCAT
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:1724553 original size:14 final size:15
Alignment explanation
Indices: 1724534--1724562 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1724524 GTGCTTCAAC
1724534 TTCTTTG-TTTTCTT
1 TTCTTTGCTTTTCTT
1724548 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
1724563 ATTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.00, C:0.17, G:0.07, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:1728810 original size:5 final size:5
Alignment explanation
Indices: 1728800--1728828 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1728790 AACTTCTTTC
1728800 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1728829 CTTCTTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:1736164 original size:6 final size:6
Alignment explanation
Indices: 1736153--1736187 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
1736143 TGCTGCAACA
1736153 AAAAAG AAAAAG AAAGAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAA-AAG AAAAAG AAAAAG AAAA
1736188 GACTCCTACA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 22 0.79
7 6 0.21
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:1736174 original size:13 final size:12
Alignment explanation
Indices: 1736153--1736187 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
1736143 TGCTGCAACA
1736153 AAAAAGAAAAAG
1 AAAAAGAAAAAG
1736165 AAAGAAGAAAAAG
1 AAA-AAGAAAAAG
1736178 AAAAAGAAAA
1 AAAAAGAAAA
1736188 GACTCCTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAG
Found at i:1739468 original size:23 final size:23
Alignment explanation
Indices: 1739413--1739468 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
1739403 TCATTCTTTT
*
1739413 TTAAAACTCAACCATTTGATAAA
1 TTAAAACTCTACCATTTGATAAA
*
1739436 TTAAAACTCTACCCTTTGATAAA
1 TTAAAACTCTACCATTTGATAAA
1739459 TTAAAACTCT
1 TTAAAACTCT
1739469 TGTGAGATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.34
Consensus pattern (23 bp):
TTAAAACTCTACCATTTGATAAA
Found at i:1742262 original size:2 final size:2
Alignment explanation
Indices: 1742255--1742309 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
1742245 ATCACCAACT
1742255 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1742297 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
1742310 TCTGCTACCA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1744531 original size:16 final size:16
Alignment explanation
Indices: 1744510--1744542 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1744500 AAGTTCTTCC
1744510 AAGATGATTCTAAGGG
1 AAGATGATTCTAAGGG
1744526 AAGATGATTCTAAGGG
1 AAGATGATTCTAAGGG
1744542 A
1 A
1744543 GTTCTTCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.30, T:0.24
Consensus pattern (16 bp):
AAGATGATTCTAAGGG
Found at i:1746943 original size:21 final size:21
Alignment explanation
Indices: 1746904--1746943 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1746894 AAGGAAGATT
*
1746904 AATGAAATGATAAAGATAAGG
1 AATGAAATGATAAAAATAAGG
1746925 AATGAAATGA-AATAAATAA
1 AATGAAATGATAA-AAATAA
1746944 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.17, T:0.20
Consensus pattern (21 bp):
AATGAAATGATAAAAATAAGG
Found at i:1746992 original size:22 final size:21
Alignment explanation
Indices: 1746966--1747006 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1746956 GCTGCGGAAT
1746966 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
1746988 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
1747007 ATGGATATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:1751075 original size:19 final size:19
Alignment explanation
Indices: 1751038--1751095 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 19
1751028 TTTGAATTTC
* *
1751038 TTTT-ATTTTATTTTATTT
1 TTTTCATTTTCTTTTCTTT
* *
1751056 TATTGATTTT-TTTTCTTT
1 TTTTCATTTTCTTTTCTTT
*
1751074 TTTTCTTTTTCTTTTCTTT
1 TTTTCATTTTCTTTTCTTT
1751093 TTT
1 TTT
1751096 AACTCCAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 17 0.52
19 16 0.48
ACGTcount: A:0.09, C:0.07, G:0.02, T:0.83
Consensus pattern (19 bp):
TTTTCATTTTCTTTTCTTT
Found at i:1761095 original size:22 final size:21
Alignment explanation
Indices: 1761058--1761098 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1761048 CCATCTCCAA
1761058 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
1761079 TTCATCCATCAAGACCATCA
1 TTCAT-CATCAACACCATCA
1761099 ATTATGCAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.34, C:0.37, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:1761397 original size:41 final size:38
Alignment explanation
Indices: 1761351--1761426 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 38
1761341 TCTCTTTTAA
*
1761351 TTTTCTTTTCTTCTTTTCTGATTTTT-TTCTTCTTTTTGTCT
1 TTTTCTTTTCTT-TTTGC--ATTTTTCTT-TTCTTTTTGTCT
1761392 TTTTCTTTTCTTTTTGCATTTTTCTTTTCTTTTTG
1 TTTTCTTTTCTTTTTGCATTTTTCTTTTCTTTTTG
1761427 CACTACAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
38 15 0.45
39 2 0.06
40 4 0.12
41 12 0.36
ACGTcount: A:0.03, C:0.16, G:0.05, T:0.76
Consensus pattern (38 bp):
TTTTCTTTTCTTTTTGCATTTTTCTTTTCTTTTTGTCT
Found at i:1761438 original size:24 final size:19
Alignment explanation
Indices: 1761351--1761428 Score: 88
Period size: 19 Copynumber: 3.9 Consensus size: 19
1761341 TCTCTTTTAA
*
1761351 TTTTCTTTTCTTCTTTTCTGAT
1 TTTTCTTTTCTT-TTTGC--AT
1761373 TTTT-TTCTTCTTTTTGTC-T
1 TTTTCTT-TTCTTTTTG-CAT
1761392 TTTTCTTTTCTTTTTGCAT
1 TTTTCTTTTCTTTTTGCAT
1761411 TTTTCTTTTCTTTTTGCA
1 TTTTCTTTTCTTTTTGCA
1761429 CTACAATTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 11
0.81 0.02 0.17
Matches are distributed among these distances:
18 1 0.02
19 33 0.65
20 2 0.04
21 5 0.10
22 10 0.20
ACGTcount: A:0.04, C:0.17, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTCTTTTCTTTTTGCAT
Found at i:1761773 original size:22 final size:21
Alignment explanation
Indices: 1761747--1761787 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1761737 GGTTGCGGAA
1761747 TTGATGGTCTTGATGGATGATG
1 TTGATGGTCTTGAT-GATGATG
* *
1761769 TTGATTGTGTTGATGATGA
1 TTGATGGTCTTGATGATGA
1761788 AACGGAGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.20, C:0.02, G:0.34, T:0.44
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGATG
Found at i:1764413 original size:2 final size:2
Alignment explanation
Indices: 1764406--1764433 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1764396 ATGAAATAAC
1764406 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
1764434 GTGTGTGTGT
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:1764438 original size:2 final size:2
Alignment explanation
Indices: 1764433--1764473 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1764423 TATATATATA
1764433 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1764474 AGAGTTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1768850 original size:35 final size:35
Alignment explanation
Indices: 1768804--1768879 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1768794 TACTATCTAT
* * *
1768804 ACCATCTTCCATCTCTATATCATGCCTATATCATC
1 ACCATCTTCCATCTCCATATCACGCCTATATAATC
*
1768839 ACCATCTTCCATCTCCATTTCACGCCTATATAATC
1 ACCATCTTCCATCTCCATATCACGCCTATATAATC
1768874 ACCATC
1 ACCATC
1768880 CCATTATCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.26, C:0.37, G:0.03, T:0.34
Consensus pattern (35 bp):
ACCATCTTCCATCTCCATATCACGCCTATATAATC
Found at i:1769034 original size:15 final size:15
Alignment explanation
Indices: 1769014--1769059 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
1769004 TTTGATATCA
1769014 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
1769029 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCC
1769044 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
1769060 TTATTTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:1772995 original size:3 final size:3
Alignment explanation
Indices: 1772987--1773014 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1772977 CCCCTGAAAG
1772987 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA A
1773015 AACCCAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:1777791 original size:16 final size:15
Alignment explanation
Indices: 1777754--1777796 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
1777744 ATATTCAAGC
1777754 ATATAAT-CTATAGTT
1 ATATAATGCT-TAGTT
1777769 ATAATAATGCTTAGCTT
1 AT-ATAATGCTTAG-TT
1777786 ATATAATGCTT
1 ATATAATGCTT
1777797 TCTTTTGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.08
16 17 0.68
17 6 0.24
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (15 bp):
ATATAATGCTTAGTT
Found at i:1778523 original size:36 final size:35
Alignment explanation
Indices: 1778425--1778535 Score: 134
Period size: 35 Copynumber: 3.2 Consensus size: 35
1778415 TTGGTATATA
* * * * *
1778425 TATAGGCGTGAAATGGTGATAGAAGAAGGTTAGGA
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
* * *
1778460 TATAGGCGTGTAATAGTAATGGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
1778495 TATAGGCGTGAAAATGGTGATGGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATGGAAGATGGTGATGT
1778531 T-TAGG
1 TATAGG
1778536 TAGTATCTTA
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 41 0.64
36 23 0.36
ACGTcount: A:0.32, C:0.03, G:0.37, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATGGAAGATGGTGATGT
Found at i:1783045 original size:36 final size:35
Alignment explanation
Indices: 1782946--1783056 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
1782936 TTGGTGGTTA
* * *
1782946 TATAGGCGTGAAATGGTGATAGAAGATGGTTAGGA
1 TATAGGCGTGAAATGGTGATAGAAGATGGTGATGT
* * *
1782981 TATAGGCGTGCAATAGTAATAGAAGATGGTGATGT
1 TATAGGCGTGAAATGGTGATAGAAGATGGTGATGT
1783016 TATAGGCGTGAAAATGGTGATAGAAGATGGTGATGT
1 TATAGGCGTG-AAATGGTGATAGAAGATGGTGATGT
1783052 T-TAGG
1 TATAGG
1783057 TAGTATCTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 43 0.65
36 23 0.35
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.28
Consensus pattern (35 bp):
TATAGGCGTGAAATGGTGATAGAAGATGGTGATGT
Found at i:1784789 original size:19 final size:19
Alignment explanation
Indices: 1784749--1784790 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
1784739 AGCATTTATC
* *
1784749 TTCATTAAAATTATGTATT
1 TTCATTAAAATCATGTAGT
1784768 TTCATTAAAAATCATGT-GT
1 TTCATT-AAAATCATGTAGT
1784787 TTCA
1 TTCA
1784791 AAGGGTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.48
Consensus pattern (19 bp):
TTCATTAAAATCATGTAGT
Found at i:1785626 original size:6 final size:6
Alignment explanation
Indices: 1785615--1785649 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
1785605 AAGTGACAAG
*
1785615 AAGAAA AAGAAA GAAGAAA AACAAA AAGAAA AAGA
1 AAGAAA AAGAAA -AAGAAA AAGAAA AAGAAA AAGA
1785650 CTCCTATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:1785630 original size:13 final size:13
Alignment explanation
Indices: 1785612--1785649 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1785602 CAAAAGTGAC
1785612 AAGAAGAAAAAGA
1 AAGAAGAAAAAGA
*
1785625 AAGAAGAAAAACA
1 AAGAAGAAAAAGA
1785638 AA-AAGAAAAAGA
1 AAGAAGAAAAAGA
1785650 CTCCTATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (13 bp):
AAGAAGAAAAAGA
Found at i:1788795 original size:22 final size:22
Alignment explanation
Indices: 1788770--1788824 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 22
1788760 GCAAGAAGAC
1788770 CCATGTGCGTTCAAGTAGGTTG
1 CCATGTGCGTTCAAGTAGGTTG
1788792 CCATGTGCAACGTTCAAGTAGGTTG
1 CCATGTG---CGTTCAAGTAGGTTG
1788817 CCATGTGC
1 CCATGTGC
1788825 AACATTCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 8 0.27
25 22 0.73
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (22 bp):
CCATGTGCGTTCAAGTAGGTTG
Found at i:1788809 original size:25 final size:25
Alignment explanation
Indices: 1788777--1788834 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
1788767 GACCCATGTG
1788777 CGTTCAAGTAGGTTGCCATGTGCAA
1 CGTTCAAGTAGGTTGCCATGTGCAA
1788802 CGTTCAAGTAGGTTGCCATGTGCAA
1 CGTTCAAGTAGGTTGCCATGTGCAA
*
1788827 CATTCAAG
1 CGTTCAAG
1788835 CATGTGCACT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (25 bp):
CGTTCAAGTAGGTTGCCATGTGCAA
Found at i:1789763 original size:28 final size:28
Alignment explanation
Indices: 1789725--1789789 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
1789715 GTAGTGTATA
*
1789725 ATGAATATTGGTTAGGAATCGATTAATG
1 ATGAATCTTGGTTAGGAATCGATTAATG
*
1789753 ATGAATCTTGGTTAGGAATTGATTAATG
1 ATGAATCTTGGTTAGGAATCGATTAATG
1789781 ATGAATCTT
1 ATGAATCTT
1789790 ATTGATGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.34, C:0.05, G:0.23, T:0.38
Consensus pattern (28 bp):
ATGAATCTTGGTTAGGAATCGATTAATG
Found at i:1801422 original size:13 final size:15
Alignment explanation
Indices: 1801403--1801436 Score: 54
Period size: 13 Copynumber: 2.4 Consensus size: 15
1801393 TACCTAATCA
1801403 ATTTTTATTT-TATT
1 ATTTTTATTTATATT
1801417 -TTTTTATTTATATT
1 ATTTTTATTTATATT
1801431 ATTTTT
1 ATTTTT
1801437 TAAAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 9 0.50
14 4 0.22
15 5 0.28
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (15 bp):
ATTTTTATTTATATT
Found at i:1801467 original size:7 final size:7
Alignment explanation
Indices: 1801455--1801577 Score: 65
Period size: 7 Copynumber: 17.4 Consensus size: 7
1801445 ATCCACATGA
1801455 AAAATAT
1 AAAATAT
1801462 AAAATAT
1 AAAATAT
*
1801469 AAAACTCT
1 AAAA-TAT
* *
1801477 AAATTTT
1 AAAATAT
*
1801484 ATAATAT
1 AAAATAT
*
1801491 ATAATAT
1 AAAATAT
1801498 -AAATAT
1 AAAATAT
*
1801504 AAAATTT
1 AAAATAT
*
1801511 ATAAATCT
1 A-AAATAT
*
1801519 AAATTAT
1 AAAATAT
* *
1801526 ATAATCT
1 AAAATAT
1801533 ACAAATA-
1 A-AAATAT
*
1801540 AAAATTT
1 AAAATAT
1801547 AAAAATAT
1 -AAAATAT
1801555 GAAAAT-T
1 -AAAATAT
1801562 AAAATA-
1 AAAATAT
*
1801568 AAATTAT
1 AAAATAT
1801575 AAA
1 AAA
1801578 TAAGTTTAAA
Statistics
Matches: 88, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
6 19 0.22
7 44 0.50
8 25 0.28
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (7 bp):
AAAATAT
Found at i:1802861 original size:32 final size:29
Alignment explanation
Indices: 1802798--1802861 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 29
1802788 AATTATTAAT
* *
1802798 AAAATTAATATTATTTTATTAATTCTATA
1 AAAATTAATATTATTTTATTAAATATATA
*
1802827 AAAATTAATATTATTGAATTATTAAATATTTA
1 AAAATTAATATTATT---TTATTAAATATATA
1802859 AAA
1 AAA
1802862 TATACTCCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 15 0.52
32 14 0.48
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (29 bp):
AAAATTAATATTATTTTATTAAATATATA
Found at i:1802907 original size:14 final size:14
Alignment explanation
Indices: 1802888--1802933 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
1802878 TAATATAATA
1802888 TAATATTTTTATTT
1 TAATATTTTTATTT
**
1802902 TAATATTAAT-TTT
1 TAATATTTTTATTT
1802915 TAATATTTTTATTT
1 TAATATTTTTATTT
1802929 TAATA
1 TAATA
1802934 AATGATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TAATATTTTTATTT
Found at i:1802944 original size:38 final size:36
Alignment explanation
Indices: 1802901--1803067 Score: 123
Period size: 41 Copynumber: 4.5 Consensus size: 36
1802891 TATTTTTATT
1802901 TTAATATTAATTTTTAATATTTTTATTTTAATAAATGA
1 TTAATA-TAATTTTTAATATTTTTATTTTAATAAAT-A
* *
1802939 TTAATATAATTATGATATATTATTCTTATTTTAATAAATAA
1 TTAATATAATT-T--T-TAATATTTTTATTTTAATAAAT-A
* * *
1802980 TTATTATAATTTATAAT-TATTTTGTTTTAATAAA-A
1 TTAATATAATTTTTAATAT-TTTTATTTTAATAAATA
*
1803015 -T-ATATTAA-TTTTAATATTTTTATTTATAA-AATTA
1 TTAATA-TAATTTTTAATATTTTTATTT-TAATAAATA
1803049 -TAGATATAATATTTTAATA
1 TTA-ATATAAT-TTTTAATA
1803068 ATAATATTGA
Statistics
Matches: 104, Mismatches: 12, Indels: 27
0.73 0.08 0.19
Matches are distributed among these distances:
33 17 0.16
34 10 0.10
35 4 0.04
36 4 0.04
37 29 0.28
38 7 0.07
40 2 0.02
41 31 0.30
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (36 bp):
TTAATATAATTTTTAATATTTTTATTTTAATAAATA
Found at i:1802951 original size:25 final size:26
Alignment explanation
Indices: 1802878--1802951 Score: 64
Period size: 27 Copynumber: 2.9 Consensus size: 26
1802868 CCTTAAAATA
**
1802878 TAATATAAT-A-TAATATTTTTATTT
1 TAATATAATGATTAATATAATTATTT
** **
1802902 TAATATTAATTTTTAATATTTTTATTT
1 TAATA-TAATGATTAATATAATTATTT
1802929 TAATA-AATGATTAATATAATTAT
1 TAATATAATGATTAATATAATTAT
1802952 GATATATTAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
24 5 0.12
25 18 0.43
27 19 0.45
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (26 bp):
TAATATAATGATTAATATAATTATTT
Found at i:1802968 original size:41 final size:37
Alignment explanation
Indices: 1802901--1803023 Score: 131
Period size: 41 Copynumber: 3.1 Consensus size: 37
1802891 TATTTTTATT
* *
1802901 TTAATATTAATTTTTAA-TATTTTTATTTTAATAAATGA
1 TTAATA-TAATTTATAATTA-TTTTATTTTAATAAATAA
1802939 TTAATATAATTATGATATATTATTCTTATTTTAATAAATAA
1 TTAATATAATT-T-ATA-ATTATT-TTATTTTAATAAATAA
* *
1802980 TTATTATAATTTATAATTATTTTGTTTTAATAAAATATA
1 TTAATATAATTTATAATTATTTTATTTTAAT-AAATA-A
1803019 TTAAT
1 TTAAT
1803024 TTTAATATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 13
0.80 0.05 0.14
Matches are distributed among these distances:
37 14 0.19
38 18 0.25
39 10 0.14
40 4 0.05
41 27 0.37
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (37 bp):
TTAATATAATTTATAATTATTTTATTTTAATAAATAA
Found at i:1802983 original size:16 final size:16
Alignment explanation
Indices: 1802964--1803002 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1802954 TATATTATTC
1802964 TTATTTTAATAAATAA
1 TTATTTTAATAAATAA
* **
1802980 TTATTATAATTTATAA
1 TTATTTTAATAAATAA
1802996 TTATTTT
1 TTATTTT
1803003 GTTTTAATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTATTTTAATAAATAA
Found at i:1805653 original size:189 final size:190
Alignment explanation
Indices: 1805328--1805687 Score: 523
Period size: 189 Copynumber: 1.9 Consensus size: 190
1805318 TTTACCATTT
*
1805328 AAACTTAAATAAGTATTATTTTAATTTGAAATATGCAAAAGTATAAAATTATCTTTAATAATCAA
1 AAACTTAAACAAGTATTATTTTAATTTGAAATATGCAAAAGTATAAAATTATCTTTAATAATCAA
* * * * * *
1805393 AGTTAAAAATGTAACAAATACATTTTTAAGTTGACATATTCAAAGAGTAATTATCATATTAATAC
66 AATTAAAAATATAACAAATACATTTTTAAATTGACATATTAAAAGAGAAATTATCATACTAATAC
1805458 TCAAATTAAATAA-TAT-ATTTAATTTGCAAT-GATCAAAAGGTAAACTCATTTTATTAGTC
131 TCAAATTAAA-AATTATCATTTAATTTGCAATAG-TCAAAAGGTAAACTCATTTTATTAGTC
* *
1805517 AAACTTAAACCAA-TATTA-TTTAATTTGAAATATGCAAAAGTATATAATTATCTTTTAATATTC
1 AAACTTAAA-CAAGTATTATTTTAATTTGAAATATGCAAAAGTATAAAATTATC-TTTAATAATC
* *
1805580 AAAATTAAAAATATAACAAATACATTTTTAAATTGACTTATTAAAAGAGAAATTATCCTACTAAT
64 AAAATTAAAAATATAACAAATACATTTTTAAATTGACATATTAAAAGAGAAATTATCATACTAAT
* * *
1805645 ATTCAAATTAAAAATTATCTTTTAATTTGTAATAGTCAAAAGG
129 ACTCAAATTAAAAATTATCATTTAATTTGCAATAGTCAAAAGG
1805688 ATTGAATTTA
Statistics
Matches: 152, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
188 35 0.23
189 94 0.62
190 22 0.14
191 1 0.01
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (190 bp):
AAACTTAAACAAGTATTATTTTAATTTGAAATATGCAAAAGTATAAAATTATCTTTAATAATCAA
AATTAAAAATATAACAAATACATTTTTAAATTGACATATTAAAAGAGAAATTATCATACTAATAC
TCAAATTAAAAATTATCATTTAATTTGCAATAGTCAAAAGGTAAACTCATTTTATTAGTC
Found at i:1809425 original size:190 final size:190
Alignment explanation
Indices: 1809124--1809492 Score: 496
Period size: 190 Copynumber: 1.9 Consensus size: 190
1809114 TCAAAAGATA
* * * * *
1809124 AAACTCCTTTTACCATTTAAACTTAAATAGGCGTTATTTTAATTTTAAATATACAAAAGTATATA
1 AAACTCATTTTACCATTCAAACTTAAATAGACATTATTTTAATTTGAAATATACAAAAGTATATA
* * * * *
1809189 ATTATCTTTAATATTCAAAGTTAAAAAGGTAACAAATACTTTTTTAAGTTGACAT-ATTCAAATA
66 ATTATCTTTAATATTCAAAGTTAAAAAGATAACAAATACTTTTTTAAATTAAC-TCATTAAAAGA
*
1809253 GTAATTATCCTACTAATATTTAAATTAAATAA-TAT-ATTTAATTTGCAATGGTACAAAGGT
130 GTAATTATCCTACTAATATTCAAATTAAA-AATTATCATTTAATTTGCAATGGTACAAAGGT
* * * * *
1809313 AAACTCATTTTACTATTCAAACTTAAATATATATTATTTTAATTTGAACTATATAAAAGTATATA
1 AAACTCATTTTACCATTCAAACTTAAATAGACATTATTTTAATTTGAAATATACAAAAGTATATA
1809378 ATTATCTTTTAATATTCAAAAG-TAAAAAGATAACAAATA-TATTTTTAAATTAACTCATTAAAA
66 ATTATC-TTTAATATTC-AAAGTTAAAAAGATAACAAATACT-TTTTTAAATTAACTCATTAAAA
* *
1809441 GAGTAATTATCGTACTAATATTCAAATTAAAAATTATCTTTTAATTTGCAAT
128 GAGTAATTATCCTACTAATATTCAAATTAAAAATTATCATTTAATTTGCAAT
1809493 AGTGGGAAGG
Statistics
Matches: 156, Mismatches: 18, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
189 65 0.42
190 74 0.47
191 17 0.11
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.40
Consensus pattern (190 bp):
AAACTCATTTTACCATTCAAACTTAAATAGACATTATTTTAATTTGAAATATACAAAAGTATATA
ATTATCTTTAATATTCAAAGTTAAAAAGATAACAAATACTTTTTTAAATTAACTCATTAAAAGAG
TAATTATCCTACTAATATTCAAATTAAAAATTATCATTTAATTTGCAATGGTACAAAGGT
Found at i:1814183 original size:3 final size:3
Alignment explanation
Indices: 1814175--1814227 Score: 65
Period size: 3 Copynumber: 17.7 Consensus size: 3
1814165 TAAATAAGAA
*
1814175 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AATT AATT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AA-T AAT AAT
1814221 AA- AAT AA
1 AAT AAT AA
1814228 AAAAGGCCCG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 4 0.09
3 34 0.76
4 7 0.16
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1814481 original size:40 final size:40
Alignment explanation
Indices: 1814429--1814650 Score: 146
Period size: 40 Copynumber: 5.4 Consensus size: 40
1814419 GTTACACGAC
* *
1814429 TCCTACGTGATGAGGAGATCTGGTCGATGGATGACACGGT
1 TCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACAGT
* * * * *
1814469 TCCTACGCGATGAGGAAGA-CTAGTTATCTATGGG-TGACA-TGAC
1 TCCTACGTGATGAGG-AGATCT-G--GTCGA-GGGATGACACAG-T
* *
1814512 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGT
1 TCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACAGT
* ** * * * * *
1814552 TCCTACGTTATGAGGAAGGCATAC-CATCTAAGGTTGACGCAGC
1 TCCTACGTGATGAGG-A-G-AT-CTGGTCGAGGGATGACACAGT
* *
1814595 TCCTACGTGATGAGGATATCTGGTCGGGGGATGACACAGT
1 TCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACAGT
*
1814635 TCCTACGCGATGAGGA
1 TCCTACGTGATGAGGA
1814651 CGGCTGGCCA
Statistics
Matches: 134, Mismatches: 34, Indels: 28
0.68 0.17 0.14
Matches are distributed among these distances:
39 4 0.03
40 65 0.49
41 6 0.04
42 6 0.04
43 50 0.37
44 3 0.02
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (40 bp):
TCCTACGTGATGAGGAGATCTGGTCGAGGGATGACACAGT
Found at i:1814519 original size:83 final size:82
Alignment explanation
Indices: 1814412--1814650 Score: 302
Period size: 83 Copynumber: 2.9 Consensus size: 82
1814402 GGTCTGGTCT
* ** *
1814412 TCTAAGGGTTACACGACTCCTACGTGATGAGGAGATCTGGTCGATGGATGACACGGTTCCTACGC
1 TCTAAGGGTGACA-GACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAGTTCCTACGC
**
1814477 GATGAGGAAGAC-TAGTTA
65 GATGAGGAAGACATA-CCA
* * *
1814495 TCTATGGGTGACATGACTCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACAGTTCCTACGT
1 TCTAAGGGTGACA-GACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAGTTCCTACGC
* *
1814560 TATGAGGAAGGCATACCA
65 GATGAGGAAGACATACCA
* *
1814578 TCTAAGGTTGAC-GCAGCTCCTACGTGATGAGGATATCTGGTCGGGGGATGACACAGTTCCTACG
1 TCTAAGGGTGACAG-A-CTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAGTTCCTACG
1814642 CGATGAGGA
64 CGATGAGGA
1814651 CGGCTGGCCA
Statistics
Matches: 135, Mismatches: 18, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
81 1 0.01
82 1 0.01
83 131 0.97
84 2 0.01
ACGTcount: A:0.25, C:0.20, G:0.32, T:0.24
Consensus pattern (82 bp):
TCTAAGGGTGACAGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACAGTTCCTACGCG
ATGAGGAAGACATACCA
Found at i:1814924 original size:132 final size:130
Alignment explanation
Indices: 1814676--1814966 Score: 318
Period size: 132 Copynumber: 2.2 Consensus size: 130
1814666 AGAGATAATG
*
1814676 GTTTCAAGAGAAACCGACTCAAAGATGATGCTTCAAGAGAAGCTGTCTCAAGAGAAACAAAATTC
1 GTTTCAAGGGAAA-CGACTCAAAGATGATGCTTCAAGAGAAGCTGTCTCAAGAGAAACAAAATTC
* * * ** * *
1814741 GTTTCAAGGGAAATGTTCTCCAAGATTCGTGTTTCAAGAGAAACAATCTCAAGGGAGAAAAAACT
65 GTTTCAAGGGAAACGTACTCAAAGATGAGTGTTTCAAGAGAAACAACCTCAAGAGAG-AAAAA-T
1814806 TT-
128 TTC
* * * * * * *
1814808 GTTTCAAGGGAAACGTTCTCAAAGATGGGTGTTTCAAGAGAA-ATCGTCTCAGGTGAGACAAAAT
1 GTTTCAAGGGAAACG-ACTCAAAGAT-GATGCTTCAAGAGAAGCT-GTCTCAAGAGAAACAAAAT
* *** *
1814872 TCGTTTCAAGGGAAACG-ACTCAAAGATGATTGTTTCAAGAGAAATTGCCTCAAGAGAGACAAAT
63 TCGTTTCAAGGGAAACGTACTCAAAGATGAGTGTTTCAAGAGAAACAACCTCAAGAGAGAAAAAT
1814936 TTC
128 TTC
*
1814939 GTTTCAAGGGAAACGACTAAAAGATGAT
1 GTTTCAAGGGAAACGACTCAAAGATGAT
1814967 CAATTTTGTT
Statistics
Matches: 132, Mismatches: 23, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
129 2 0.02
130 11 0.08
131 21 0.16
132 53 0.40
133 45 0.34
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.24
Consensus pattern (130 bp):
GTTTCAAGGGAAACGACTCAAAGATGATGCTTCAAGAGAAGCTGTCTCAAGAGAAACAAAATTCG
TTTCAAGGGAAACGTACTCAAAGATGAGTGTTTCAAGAGAAACAACCTCAAGAGAGAAAAATTTC
Found at i:1814966 original size:65 final size:65
Alignment explanation
Indices: 1814676--1814965 Score: 314
Period size: 65 Copynumber: 4.4 Consensus size: 65
1814666 AGAGATAATG
* * * *
1814676 GTTTCAAGAGAAACCGACTCAAAGATGA-TGCTTCAAGAGAAGCTGTCTCAAGAGAAACAAAATT
1 GTTTCAAGGGAAA-CGACTCAAAGATGAGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
1814740 C
65 C
* * * ** ** * *
1814741 GTTTCAAGGGAAATGTTCTCCAAGATTCGTGTTTCAAGAGAAACAATCTCAAGGGAGAAAAAACT
1 GTTTCAAGGGAAACG-ACTCAAAGATGAGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-T
*
1814806 TT
64 TC
* * * *
1814808 GTTTCAAGGGAAACGTTCTCAAAGATGGGTGTTTCAAGAGAAA-TCGTCTCAGGTGAGACAAAAT
1 GTTTCAAGGGAAACG-ACTCAAAGATGAGTGTTTCAAGAGAAACT-GTCTCAAGAGAGACAAAAT
1814872 TC
64 TC
* * * *
1814874 GTTTCAAGGGAAACGACTCAAAGATGATTGTTTCAAGAGAAATTGCCTCAAGAGAGACAAATTTC
1 GTTTCAAGGGAAACGACTCAAAGATGAGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTC
*
1814939 GTTTCAAGGGAAACGACTAAAAGATGA
1 GTTTCAAGGGAAACGACTCAAAGATGA
1814966 TCAATTTTGT
Statistics
Matches: 188, Mismatches: 32, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
64 1 0.01
65 87 0.46
66 45 0.24
67 55 0.29
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (65 bp):
GTTTCAAGGGAAACGACTCAAAGATGAGTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTC
Found at i:1815061 original size:36 final size:38
Alignment explanation
Indices: 1814996--1815067 Score: 94
Period size: 36 Copynumber: 1.9 Consensus size: 38
1814986 ACAATTTCCG
* * *
1814996 AATTTGTGTTTTAAAGAAAAACTATCTCAAGTGAGACGA
1 AATTTGTGTTTGAAAG-AAAACAATCTCAAATGAGACGA
1815035 AATTTGT-TTTGAAAG-AAACAATCTCAAATGAGA
1 AATTTGTGTTTGAAAGAAAACAATCTCAAATGAGA
1815068 TTAATTTTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 16 0.53
38 7 0.23
39 7 0.23
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (38 bp):
AATTTGTGTTTGAAAGAAAACAATCTCAAATGAGACGA
Found at i:1815077 original size:36 final size:36
Alignment explanation
Indices: 1814994--1815079 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 36
1814984 AAACAATTTC
* *
1814994 CGAATTTGTGTTTTAAAGAAAAACTATCTCAAGTGAGA
1 CGAATTT-TGTTTTAAAG-AAAACAATCTCAAATGAGA
*
1815032 CGAAATTTGTTTTGAAAG-AAACAATCTCAAATGAGA
1 CGAATTTTGTTTT-AAAGAAAACAATCTCAAATGAGA
**
1815068 TTAATTTTGTTT
1 CGAATTTTGTTT
1815080 CAAGTAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
36 25 0.61
37 6 0.15
38 10 0.24
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (36 bp):
CGAATTTTGTTTTAAAGAAAACAATCTCAAATGAGA
Found at i:1815079 original size:102 final size:102
Alignment explanation
Indices: 1814968--1815163 Score: 243
Period size: 102 Copynumber: 1.9 Consensus size: 102
1814958 AAAGATGATC
* * * **
1814968 AATTTTGTTTCCAGTGAAACAA-TTTCCGAATTTGTGTTTTAAAGAAAAACTATCTCAAGTGAGA
1 AATTTTGTTTCAAGTAAAACAACTTTCAGAATTTGTGTTCCAAAGAAAAA-TATCTCAAGTGA-A
* *
1815032 -CGAAATTTGTTTTGAAAGAAACAATCTCAAATGAGATT
64 TCAAAATTTGCTTTGAAAGAAACAATCTCAAATGAGATT
* * * * * *
1815070 AATTTTGTTTCAAGTAAAATAACTTTTATAATTTGTGTTCCAAGGGAAAATGTCTCAAGTGAATC
1 AATTTTGTTTCAAGTAAAACAACTTTCAGAATTTGTGTTCCAAAGAAAAATATCTCAAGTGAATC
1815135 AAAATTTGCTTTGAAAGAAACAATCTCAA
66 AAAATTTGCTTTGAAAGAAACAATCTCAA
1815164 GTAAGACAAA
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
101 1 0.01
102 58 0.73
103 20 0.25
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.35
Consensus pattern (102 bp):
AATTTTGTTTCAAGTAAAACAACTTTCAGAATTTGTGTTCCAAAGAAAAATATCTCAAGTGAATC
AAAATTTGCTTTGAAAGAAACAATCTCAAATGAGATT
Found at i:1815237 original size:37 final size:37
Alignment explanation
Indices: 1815158--1815237 Score: 90
Period size: 37 Copynumber: 2.2 Consensus size: 37
1815148 AAAGAAACAA
*
1815158 TCTCAAGTAAGACAAAATTTATTTTTAGAGAAAACTG
1 TCTCAAGCAAGACAAAATTTATTTTTAGAGAAAACTG
* * * * *
1815195 CCTCAAGCGAGACAAACTTTGTTTTTA-AGAAAAATTG
1 TCTCAAGCAAGACAAAATTTATTTTTAGAG-AAAACTG
1815232 TCTCAA
1 TCTCAA
1815238 AAGCGACATG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
36 2 0.06
37 33 0.94
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (37 bp):
TCTCAAGCAAGACAAAATTTATTTTTAGAGAAAACTG
Found at i:1816432 original size:15 final size:14
Alignment explanation
Indices: 1816400--1816488 Score: 81
Period size: 15 Copynumber: 6.2 Consensus size: 14
1816390 CATGTACTTC
* *
1816400 TTGTTCTTTTTTTAT
1 TTGTT-TTTTTCTCT
1816415 TTGTTTTTCTTCTCT
1 TTGTTTTT-TTCTCT
*
1816430 TTGTTTTTTCTCTAT
1 TTGTTTTTT-TCTCT
*
1816445 TTGTTTCTTTCTCT
1 TTGTTTTTTTCTCT
*
1816459 TTGTTGTTTT-TCT
1 TTGTTTTTTTCTCT
**
1816472 TTCCTTTTTTCTCT
1 TTGTTTTTTTCTCT
1816486 TTG
1 TTG
1816489 CTCTTTGTTT
Statistics
Matches: 60, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
13 10 0.17
14 21 0.35
15 29 0.48
ACGTcount: A:0.02, C:0.16, G:0.08, T:0.74
Consensus pattern (14 bp):
TTGTTTTTTTCTCT
Found at i:1816472 original size:19 final size:18
Alignment explanation
Indices: 1816448--1816509 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
1816438 TCTCTATTTG
1816448 TTTCTTTCTCTTTGTTGTT
1 TTTCTTTCTCTTTGTT-TT
1816467 TTTCTTTC-C--T-TTTT
1 TTTCTTTCTCTTTGTTTT
*
1816481 TCTCTTTGCTCTTTGTTTTT
1 TTTCTTT-CTCTTTG-TTTT
1816501 TTTCTTTCT
1 TTTCTTTCT
1816510 GTGCTTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 12
0.71 0.04 0.24
Matches are distributed among these distances:
14 8 0.23
15 3 0.09
16 2 0.06
18 2 0.06
19 10 0.29
20 10 0.29
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.74
Consensus pattern (18 bp):
TTTCTTTCTCTTTGTTTT
Found at i:1816494 original size:21 final size:20
Alignment explanation
Indices: 1816469--1816507 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1816459 TTGTTGTTTT
1816469 TCTTTCCTTTTTTCTCTTTGC
1 TCTTT-CTTTTTTCTCTTTGC
* *
1816490 TCTTTGTTTTTTTTCTTT
1 TCTTTCTTTTTTCTCTTT
1816508 CTGTGCTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (20 bp):
TCTTTCTTTTTTCTCTTTGC
Found at i:1819904 original size:22 final size:22
Alignment explanation
Indices: 1819874--1819948 Score: 116
Period size: 22 Copynumber: 3.5 Consensus size: 22
1819864 CATCAATGTA
1819874 GTTG-TGTCTCTCTTCTTTCTT
1 GTTGTTGTCTCTCTTCTTTCTT
* *
1819895 GTTGTTGTCTCTTTTCTTTTTT
1 GTTGTTGTCTCTCTTCTTTCTT
*
1819917 GTTGTTGTCTTTCTTCTTTCTT
1 GTTGTTGTCTCTCTTCTTTCTT
1819939 GTTGTTGTCT
1 GTTGTTGTCT
1819949 TTTGTTTGTT
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 4 0.08
22 44 0.92
ACGTcount: A:0.00, C:0.17, G:0.16, T:0.67
Consensus pattern (22 bp):
GTTGTTGTCTCTCTTCTTTCTT
Found at i:1820468 original size:19 final size:19
Alignment explanation
Indices: 1820446--1820490 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
1820436 GCTTCCAATT
1820446 ATAATATTATTTAATAT-TA
1 ATAATATTA-TTAATATATA
* *
1820465 ATAATAATATTATTATATA
1 ATAATATTATTAATATATA
1820484 ATAATAT
1 ATAATAT
1820491 ACATAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
ATAATATTATTAATATATA
Found at i:1820473 original size:22 final size:19
Alignment explanation
Indices: 1820446--1820489 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
1820436 GCTTCCAATT
1820446 ATAATATTATTTAATATTAATA
1 ATAATATTA-TT-ATA-TAATA
1820468 ATAATATTATTATATAATA
1 ATAATATTATTATATAATA
1820487 ATA
1 ATA
1820490 TACATAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
20 3 0.14
21 2 0.09
22 9 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAATATTATTATATAATA
Found at i:1820484 original size:16 final size:15
Alignment explanation
Indices: 1820460--1820490 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1820450 TATTATTTAA
1820460 TATTAATAATAATAT
1 TATTAATAATAATAT
1820475 TATTATATAATAATAT
1 TATTA-ATAATAATAT
1820491 ACATAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTAATAATAATAT
Found at i:1820485 original size:25 final size:25
Alignment explanation
Indices: 1820450--1820501 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
1820440 CCAATTATAA
* *
1820450 TATTATTTAATATTAATA-ATAATAT
1 TATTATATAATAAT-ATACATAATAT
1820475 TATTATATAATAATATACATAATAT
1 TATTATATAATAATATACATAATAT
1820500 TA
1 TA
1820502 ACGTTACTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TATTATATAATAATATACATAATAT
Found at i:1820944 original size:175 final size:175
Alignment explanation
Indices: 1820724--1821626 Score: 1423
Period size: 175 Copynumber: 5.2 Consensus size: 175
1820714 AAATAACTTG
** * * * * * *
1820724 CTTCACTACTCTTATGTAAAGGCTGAATTGCATTACTTCATTACTCTTTCATGAAGGCTTAATAC
1 CTTCACTACTCTTCCGTGAAGGTTGAGTTGCATTGCTTCATTACTCTTTCATGAAGGTTTCATAC
*
1820789 TTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGGAAATAATCTT
66 TTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGGAAAGAATCTT
*
1820854 TATACTTCACTACTCTTTCGTGAAGGCTGATTCAAGGTTGGAATA
131 TCTACTTCACTACTCTTTCGTGAAGGCTGATTCAAGGTTGGAATA
* *
1820899 CTTCATTACTCTTCCGTGAAGGTTGAGTTGCATTGCTTCATTACTCTTTCATGAAGGCTTCATAC
1 CTTCACTACTCTTCCGTGAAGGTTGAGTTGCATTGCTTCATTACTCTTTCATGAAGGTTTCATAC
* *
1820964 TTTGCTG-AAAATTCGTTCCACTACTCTTCCGTGGAGAGCGAATTATGATCTTGGAAAGAATCTT
66 TTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGGAAAGAATCTT
* *
1821028 TCTACTTCACTACTCTTTTGTGAAGGCTGATTCAAGTTTGGAATA
131 TCTACTTCACTACTCTTTCGTGAAGGCTGATTCAAGGTTGGAATA
*
1821073 CTTCACTACTCTTCGGTGAAGGTTTG-GTTGCATTGCTTCATTACTCTTTCATGAAGGTTTCATA
1 CTTCACTACTCTTCCGTGAAGG-TTGAGTTGCATTGCTTCATTACTCTTTCATGAAGGTTTCATA
* * *
1821137 CTTTACTGAAAAATCCATTCCACTACTCTTCCGTGGAGAGCGAATTATGATCTTGGAAAGAATCT
65 CTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGGAAAGAATCT
* *
1821202 TTCTACTTCACTACTCTTTCGTGAAGGATGATTCAAGGTTAGAATA
130 TTCTACTTCACTACTCTTTCGTGAAGGCTGATTCAAGGTTGGAATA
* *
1821248 CTTCACTACTCTTTCGTGAAGGTTGAGTTGCATTGCTTCATTACTATTTCATGAAGGTTTCATAC
1 CTTCACTACTCTTCCGTGAAGGTTGAGTTGCATTGCTTCATTACTCTTTCATGAAGGTTTCATAC
* *
1821313 TTTGCTGAAAAATCCGTTCCACTACTCTTCTGTGGAGAGCGAATTTTGATTTTGGAAAGAATCTT
66 TTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGGAAAGAATCTT
* * * * *
1821378 TCTACTTCACTATTTTTTTGTGAAGGCTGATTCAAGGTTAGAATG
131 TCTACTTCACTACTCTTTCGTGAAGGCTGATTCAAGGTTGGAATA
*
1821423 CTTCACTACTCTTCCGTGAAGGTTGAGTTGTATTGCTTCATTACTCTTTCATGAAGGTTTCATAC
1 CTTCACTACTCTTCCGTGAAGGTTGAGTTGCATTGCTTCATTACTCTTTCATGAAGGTTTCATAC
* * *
1821488 TTTGCTGAAAAATCCGTTCCACTAATCTTCCGTGGAGAGCAAATTTTGATCTTGGAAAGAATATT
66 TTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGGAAAGAATCTT
* * *
1821553 TCTACTTCACTACTCTTTCATTAAGGCTGATTCCAGGTTGGAATA
131 TCTACTTCACTACTCTTTCGTGAAGGCTGATTCAAGGTTGGAATA
**
1821598 CTTCACTACTCTTCTATGAAGGTTGAGTT
1 CTTCACTACTCTTCCGTGAAGGTTGAGTT
1821627 AACTTAAGAA
Statistics
Matches: 670, Mismatches: 55, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
174 163 0.24
175 507 0.76
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (175 bp):
CTTCACTACTCTTCCGTGAAGGTTGAGTTGCATTGCTTCATTACTCTTTCATGAAGGTTTCATAC
TTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGAGCGAATTTTGATCTTGGAAAGAATCTT
TCTACTTCACTACTCTTTCGTGAAGGCTGATTCAAGGTTGGAATA
Found at i:1821685 original size:20 final size:20
Alignment explanation
Indices: 1821660--1821746 Score: 104
Period size: 20 Copynumber: 4.3 Consensus size: 20
1821650 CGAGAGACTG
* *
1821660 ACAAATGACCCAAAGGATTT
1 ACAAATGACCCGAAGGCTTT
* *
1821680 ACAAATTACCTGAAGGCTTT
1 ACAAATGACCCGAAGGCTTT
*
1821700 ACAAATGAGCCTG-AGGCTTT
1 ACAAATGA-CCCGAAGGCTTT
*
1821720 ACAAATGACCCGGAGGCTTT
1 ACAAATGACCCGAAGGCTTT
1821740 ACAAATG
1 ACAAATG
1821747 GTGGGAAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
19 3 0.05
20 52 0.88
21 4 0.07
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.23
Consensus pattern (20 bp):
ACAAATGACCCGAAGGCTTT
Found at i:1828472 original size:13 final size:13
Alignment explanation
Indices: 1828449--1828495 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 13
1828439 AATATAGATA
1828449 AATACTAAATATTT
1 AATA-TAAATATTT
1828463 AATATAAATATTATT
1 AATATAAATA-T-TT
1828478 AAT-TATAATATTT
1 AATATA-AATATTT
1828491 AATAT
1 AATAT
1828496 TAAAATCATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.38
14 9 0.31
15 9 0.31
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATAAATATTT
Found at i:1828497 original size:15 final size:14
Alignment explanation
Indices: 1828449--1828499 Score: 52
Period size: 14 Copynumber: 3.6 Consensus size: 14
1828439 AATATAGATA
*
1828449 AATACTAAATATTT
1 AATATTAAATATTT
1828463 AATA-TAAATA-TT
1 AATATTAAATATTT
*
1828475 ATTAATTATAATATTT
1 AAT-ATTA-AATATTT
1828491 AATATTAAA
1 AATATTAAA
1828500 ATCATATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 4 0.13
13 7 0.23
14 8 0.26
15 8 0.26
16 4 0.13
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
AATATTAAATATTT
Found at i:1829310 original size:22 final size:22
Alignment explanation
Indices: 1829277--1829347 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
1829267 AATGTTGTTG
* *
1829277 TGTCTCTTTTCTTTCTT-ACTTT
1 TGTCTCTCTTCTTTCTTGA-TGT
*
1829299 TTTCTCTCTTCTTTCTTGATGT
1 TGTCTCTCTTCTTTCTTGATGT
**
1829321 TGTCTCTCTTCTTTCTTTTTGT
1 TGTCTCTCTTCTTTCTTGATGT
1829343 TGTCT
1 TGTCT
1829348 TGTGTTTTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 41 0.98
23 1 0.02
ACGTcount: A:0.03, C:0.23, G:0.08, T:0.66
Consensus pattern (22 bp):
TGTCTCTCTTCTTTCTTGATGT
Found at i:1829590 original size:16 final size:17
Alignment explanation
Indices: 1829564--1829595 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1829554 CGGTGGAGAG
1829564 ATGATAACCCTAGGGTA
1 ATGATAACCCTAGGGTA
1829581 ATGA-AACCCTAGGGT
1 ATGATAACCCTAGGGT
1829596 TCCTGCTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.22
Consensus pattern (17 bp):
ATGATAACCCTAGGGTA
Found at i:1829897 original size:25 final size:30
Alignment explanation
Indices: 1829839--1829902 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 30
1829829 CTTCCATTTG
1829839 TAATATTAATTAATATTAATAATATTAATAA
1 TAATATT-ATTAATATTAATAATATTAATAA
1829870 TAATATTATT-ATA-TAATAATA-T-AT-A
1 TAATATTATTAATATTAATAATATTAATAA
1829895 TAATATTA
1 TAATATTA
1829903 ACGTTACTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.27
26 2 0.06
27 1 0.03
28 8 0.24
29 3 0.09
30 3 0.09
31 7 0.21
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (30 bp):
TAATATTATTAATATTAATAATATTAATAA
Found at i:1843385 original size:15 final size:15
Alignment explanation
Indices: 1843365--1843399 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1843355 TGTTAACCAA
1843365 TGTTTTTGTTGATTG
1 TGTTTTTGTTGATTG
1843380 TGTTTTTGTTGATTG
1 TGTTTTTGTTGATTG
1843395 TGTTT
1 TGTTT
1843400 CTGTGTTTAA
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:0.06, C:0.00, G:0.26, T:0.69
Consensus pattern (15 bp):
TGTTTTTGTTGATTG
Found at i:1851324 original size:107 final size:107
Alignment explanation
Indices: 1851139--1851362 Score: 387
Period size: 107 Copynumber: 2.1 Consensus size: 107
1851129 GAATGAGCAT
* * *
1851139 TATGTGTGCAACCTAATAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAAC
1 TATGTGTGCAACCTAAAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATATGTGTGCAAC
*
1851204 CTAAGAAATTCATAATAAGTTTATGAAT-TCCGTATTGGCAC
66 CTAAGAAATTCATAATAAGTATATGAATATCCGTATTGGCAC
1851245 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATATGTGTGCAA
1 TATGTGTGCAACCTAA-AAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATATGTGTGCAA
*
1851310 CCTAAGAAATTCATAATTAGTATATGAATATCCGTATTGGCAC
65 CCTAAGAAATTCATAATAAGTATATGAATATCCGTATTGGCAC
1851353 TATGTGTGCA
1 TATGTGTGCA
1851363 CCCCACGTAA
Statistics
Matches: 111, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
106 16 0.14
107 72 0.65
108 23 0.21
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (107 bp):
TATGTGTGCAACCTAAAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATATGTGTGCAAC
CTAAGAAATTCATAATAAGTATATGAATATCCGTATTGGCAC
Found at i:1851376 original size:54 final size:54
Alignment explanation
Indices: 1851139--1851362 Score: 380
Period size: 54 Copynumber: 4.2 Consensus size: 54
1851129 GAATGAGCAT
* *
1851139 TATGTGTGCAACCTAA-TAATTCATAATAAGTTTATGAATTTTCGTATTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
1851192 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAA-TTCCGTATTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
*
1851245 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAA
1 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
* * *
1851299 TATGTGTGCAACCTAAGAAATTCATAATTAGTATATGAATATCCGTATTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
1851353 TATGTGTGCA
1 TATGTGTGCA
1851363 CCCCACGTAA
Statistics
Matches: 162, Mismatches: 7, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
53 68 0.42
54 94 0.58
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (54 bp):
TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAC
Found at i:1851400 original size:54 final size:53
Alignment explanation
Indices: 1851139--1851413 Score: 365
Period size: 54 Copynumber: 5.2 Consensus size: 53
1851129 GAATGAGCAT
*
1851139 TATGTGTGCAACCTAA-TAATTCATAATAAGTTTATGAATTTTCGTATTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAA-TTTCGTATTGGCAC
*
1851192 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTCCGTATTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCGTATTGGCAC
*
1851245 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAA
1 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTT-CGTATTGGCAC
* * *
1851299 TATGTGTGCAACCTAAGAAATTCATAATTAGTATATGAATATCCGTATTGGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT-TTCGTATTGGCAC
* * * * * * * **
1851353 TATGTGTGCACCCCACGTAATTCACAATGAGTTTGTGAATTATCGTATCCGCAC
1 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATT-TCGTATTGGCAC
1851407 -ATGTGTG
1 TATGTGTG
1851414 TGAAAACCAC
Statistics
Matches: 199, Mismatches: 19, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
53 78 0.39
54 120 0.60
55 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (53 bp):
TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCGTATTGGCAC
Found at i:1851413 original size:107 final size:105
Alignment explanation
Indices: 1851139--1851413 Score: 372
Period size: 107 Copynumber: 2.6 Consensus size: 105
1851129 GAATGAGCAT
*
1851139 TATGTGTGCAACCTAA-TAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAA
1 TATGTGTGCAACCCAAGTAATTCATAATAAGTTTATGAA-TTTCGTATTGGCAC-ATGTGTGCAA
*
1851203 CCTAAGAAATTCATAATAAGTTTATGAATTCCGTATTGGCAC
64 CCTAAGAAATTCATAATAAGTATATGAATTCCGTATTGGCAC
* * *
1851245 TATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATATGTGTGCAA
1 TATGTGTGCAACCCAAGTAATTCATAATAAGTTTATGAATTT-CGTATTGGC-ACATGTGTGCAA
*
1851310 CCTAAGAAATTCATAATTAGTATATGAATATCCGTATTGGCAC
64 CCTAAGAAATTCATAATAAGTATATGAAT-TCCGTATTGGCAC
* * * * * **
1851353 TATGTGTGCACCCCACGTAATTCACAATGAGTTTGTGAATTATCGTATCCGCACATGTGTG
1 TATGTGTGCAACCCAAGTAATTCATAATAAGTTTATGAATT-TCGTATTGGCACATGTGTG
1851414 TGAAAACCAC
Statistics
Matches: 150, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
106 19 0.13
107 75 0.50
108 55 0.37
109 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (105 bp):
TATGTGTGCAACCCAAGTAATTCATAATAAGTTTATGAATTTCGTATTGGCACATGTGTGCAACC
TAAGAAATTCATAATAAGTATATGAATTCCGTATTGGCAC
Found at i:1853549 original size:40 final size:40
Alignment explanation
Indices: 1853484--1853681 Score: 132
Period size: 40 Copynumber: 4.9 Consensus size: 40
1853474 AAATACTAGT
* *
1853484 AAATACTTGTATTTTAGTGGTGTTTTTATATAAACGCCACA
1 AAATA-TTGTACTTTAGTGGAGTTTTTATATAAACGCCACA
* * * * *
1853525 AAATATTGTACTTTATTGGAGTTTTTGTATAAATGCCGCT
1 AAATATTGTACTTTAGTGGAGTTTTTATATAAACGCCACA
* * * * * * **
1853565 AAATATTGTAC--TAGCGGCGTTTTAAGCACAAACACCATT
1 AAATATTGTACTTTAGTGGAGTTTTTA-TATAAACGCCACA
* * * **** *
1853604 AAATACTCGTACTTCAGTGGCGTTTTTATATAAACAATGCT
1 AAATA-TTGTACTTTAGTGGAGTTTTTATATAAACGCCACA
1853645 AAATATTGTACTTTAGTGGCA-TTTTTATATAAACGCC
1 AAATATTGTACTTTAGTGG-AGTTTTTATATAAACGCC
1853682 GCTAAAGACC
Statistics
Matches: 118, Mismatches: 34, Indels: 11
0.72 0.21 0.07
Matches are distributed among these distances:
38 9 0.08
39 12 0.10
40 69 0.58
41 17 0.14
42 11 0.09
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (40 bp):
AAATATTGTACTTTAGTGGAGTTTTTATATAAACGCCACA
Found at i:1853670 original size:120 final size:120
Alignment explanation
Indices: 1853456--1853687 Score: 295
Period size: 120 Copynumber: 1.9 Consensus size: 120
1853446 AATGGGTTTT
* * * * * * * **
1853456 TAGCGGCGTTTTTAGAACAAATACTAGTAAATACTTGTATTTTAGTGGTGTTTTTATATAAACGC
1 TAGCGGCGTTTTAAGAACAAACACCAGTAAATACTCGTACTTCAGTGGCGTTTTTATATAAACAA
* * *
1853521 CACAAAATATTGTACTTTATTGGAGTTTTTGTATAAATGCCGCTAAATATTGTAC
66 CACAAAATATTGTACTTTAGTGGAGTTTTTATATAAACGCCGCTAAATATTGTAC
* *
1853576 TAGCGGCGTTTTAAGCACAAACACCATTAAATACTCGTACTTCAGTGGCGTTTTTATATAAACAA
1 TAGCGGCGTTTTAAGAACAAACACCAGTAAATACTCGTACTTCAGTGGCGTTTTTATATAAACAA
** *
1853641 TGCTAAATATTGTACTTTAGTGGCA-TTTTTATATAAACGCCGCTAAA
66 CACAAAATATTGTACTTTAGTGG-AGTTTTTATATAAACGCCGCTAAA
1853688 GACCCATACT
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
120 93 0.99
121 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (120 bp):
TAGCGGCGTTTTAAGAACAAACACCAGTAAATACTCGTACTTCAGTGGCGTTTTTATATAAACAA
CACAAAATATTGTACTTTAGTGGAGTTTTTATATAAACGCCGCTAAATATTGTAC
Found at i:1853686 original size:40 final size:41
Alignment explanation
Indices: 1853483--1853847 Score: 177
Period size: 41 Copynumber: 9.0 Consensus size: 41
1853473 CAAATACTAG
* ** *
1853483 TAAATACTTGTATTTTAGTGGTGTTTTTATATAAACGCCAC
1 TAAATACTTGTACTTTAGTGGCATTTTTATATAAACGCCGC
* * * *
1853524 AAAATA-TTGTACTTTATTGG-AGTTTTTGTATAAATGCCGC
1 TAAATACTTGTACTTTAGTGGCA-TTTTTATATAAACGCCGC
* * * * * * **
1853564 TAAATA-TTGTAC--TAGCGGCGTTTTAAGCACAAACACCAT
1 TAAATACTTGTACTTTAGTGGCATTTTTA-TATAAACGCCGC
* * * ***
1853603 TAAATACTCGTACTTCAGTGGCGTTTTTATATAAACAATGC
1 TAAATACTTGTACTTTAGTGGCATTTTTATATAAACGCCGC
1853644 TAAATA-TTGTACTTTAGTGGCATTTTTATATAAACGCCGC
1 TAAATACTTGTACTTTAGTGGCATTTTTATATAAACGCCGC
* *** * * *** *
1853684 TAAAGACCCATACTTTAGTGGAATTTTTATACAAATATCGT
1 TAAATACTTGTACTTTAGTGGCATTTTTATATAAACGCCGC
* ** * * **
1853725 TAAAGACTCATACTTTAGTGGCGTTTTTATACAAATTCCGC
1 TAAATACTTGTACTTTAGTGGCATTTTTATATAAACGCCGC
* ** * ** * * *
1853766 CAAATACTCATACTATAGTGGCGCTTTTATACAAACCCCAC
1 TAAATACTTGTACTTTAGTGGCATTTTTATATAAACGCCGC
* * * *
1853807 CAAAGACTCGTACTTTAGTGGCGTTTTT-TGAATAAACGCCG
1 TAAATACTTGTACTTTAGTGGCATTTTTAT--ATAAACGCCG
1853848 TAATTTATCA
Statistics
Matches: 250, Mismatches: 65, Indels: 17
0.75 0.20 0.05
Matches are distributed among these distances:
38 8 0.03
39 12 0.05
40 77 0.31
41 135 0.54
42 18 0.07
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.36
Consensus pattern (41 bp):
TAAATACTTGTACTTTAGTGGCATTTTTATATAAACGCCGC
Found at i:1853753 original size:82 final size:82
Alignment explanation
Indices: 1853653--1853847 Score: 203
Period size: 82 Copynumber: 2.4 Consensus size: 82
1853643 CTAAATATTG
* * * *
1853653 TACTTTAGTGGCATTTTTATATAAACGCCGCTAAAGACCCATACTTTAGTGGAATTTTTATACAA
1 TACTTTAGTGGCGTTTTTATATAAACGCCGCCAAAGACCCATACTATAGTGGAACTTTTATACAA
* * ***
1853718 ATATCGTTAAAGACTCA
66 ACACCACCAAAGACTCA
* ** * * **
1853735 TACTTTAGTGGCGTTTTTATACAAATTCCGCCAAATACTCATACTATAGTGGCGCTTTTATACAA
1 TACTTTAGTGGCGTTTTTATATAAACGCCGCCAAAGACCCATACTATAGTGGAACTTTTATACAA
* *
1853800 ACCCCACCAAAGACTCG
66 ACACCACCAAAGACTCA
1853817 TACTTTAGTGGCGTTTTT-TGAATAAACGCCG
1 TACTTTAGTGGCGTTTTTAT--ATAAACGCCG
1853848 TAATTTATCA
Statistics
Matches: 90, Mismatches: 21, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
81 1 0.01
82 82 0.91
83 7 0.08
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.34
Consensus pattern (82 bp):
TACTTTAGTGGCGTTTTTATATAAACGCCGCCAAAGACCCATACTATAGTGGAACTTTTATACAA
ACACCACCAAAGACTCA
Found at i:1853756 original size:41 final size:40
Alignment explanation
Indices: 1853653--1853834 Score: 184
Period size: 41 Copynumber: 4.5 Consensus size: 40
1853643 CTAAATATTG
* * * *
1853653 TACTTTAGTGGCATTTTTATATAAACGCCGCTAAAGACCCA
1 TACTTTAGTGGCGTTTTTATACAAAC-CCGCCAAAGACTCA
** ** **
1853694 TACTTTAGTGGAATTTTTATACAAATATCGTTAAAGACTCA
1 TACTTTAGTGGCGTTTTTATACAAA-CCCGCCAAAGACTCA
* *
1853735 TACTTTAGTGGCGTTTTTATACAAATTCCGCCAAATACTCA
1 TACTTTAGTGGCGTTTTTATACAAA-CCCGCCAAAGACTCA
* * * *
1853776 TACTATAGTGGCGCTTTTATACAAACCCCACCAAAGACTCG
1 TACTTTAGTGGCGTTTTTATACAAA-CCCGCCAAAGACTCA
1853817 TACTTTAGTGGCGTTTTT
1 TACTTTAGTGGCGTTTTT
1853835 TGAATAAACG
Statistics
Matches: 118, Mismatches: 22, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
41 118 1.00
ACGTcount: A:0.30, C:0.20, G:0.14, T:0.35
Consensus pattern (40 bp):
TACTTTAGTGGCGTTTTTATACAAACCCGCCAAAGACTCA
Done.