Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001840.1 Hibiscus syriacus cultivar Beakdansim tig00003725_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: 2412736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1464718 original size:23 final size:23
Alignment explanation
Indices: 1464692--1464740 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
1464682 GAGAAGATCG
* *
1464692 AAAACATGTCAAAAAGTCATAGA
1 AAAACATGTCAAAAAGACAGAGA
*
1464715 AAAACATGTCACAAAGACAGAGA
1 AAAACATGTCAAAAAGACAGAGA
1464738 AAA
1 AAA
1464741 TCGCGCCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.12
Consensus pattern (23 bp):
AAAACATGTCAAAAAGACAGAGA
Found at i:1467913 original size:3 final size:3
Alignment explanation
Indices: 1467894--1467959 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
1467884 TTTTATTGTT
* * * *
1467894 TTA TT- TTA TTT TTA TTA TTA TAA TTA TTAA ATA TTA GATA TTAA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA -TTA TT-A TTA
1467940 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
1467960 TTTAGGTCAT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
2 4 0.08
3 39 0.78
4 7 0.14
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1469360 original size:2 final size:2
Alignment explanation
Indices: 1469353--1469392 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1469343 TTACAAATTA
1469353 AT AT 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 AT AT
1469393 GTTGGGTATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1469912 original size:80 final size:80
Alignment explanation
Indices: 1469828--1470065 Score: 195
Period size: 80 Copynumber: 3.1 Consensus size: 80
1469818 TGGTAATTTT
1469828 AATTTAATTTATTTGGTTGCTTTTGAATATTATTAAATTCACATTTTTGTTTTATGGGATCAAAA
1 AATTTAATTTATTTGGTTGCTTTTGAATATTATTAAATTCACATTTTTGTTTTATGGGATCAAAA
1469893 ATTAAATTAAGTTCG
66 ATTAAATTAAGTTCG
* * * *
1469908 AATTT-A--TATCTGG-T-C--TCG-ATATT-TGTAAATAATCGAACATTCTTTATCTTTCT---
1 AATTTAATTTATTTGGTTGCTTTTGAATATTAT-TAAAT--TC--ACATT-TTTGT-TTTATGGG
* ** **
1469961 A--AAACGACTT--GGTAA-TTTT
59 ATCAAA--AATTAAATTAAGTTCG
1469980 AATTTAATTTATTTGGTTGCTTTTGAATATTATTAAATTCACATTTTTGTTTTATGGGATCAAAA
1 AATTTAATTTATTTGGTTGCTTTTGAATATTATTAAATTCACATTTTTGTTTTATGGGATCAAAA
1470045 ATTAAATTAAGTTCG
66 ATTAAATTAAGTTCG
1470060 AATTTA
1 AATTTA
1470066 TAAAGTTAAT
Statistics
Matches: 114, Mismatches: 18, Indels: 52
0.62 0.10 0.28
Matches are distributed among these distances:
71 1 0.01
72 17 0.15
73 9 0.08
74 6 0.05
75 15 0.13
76 12 0.11
77 15 0.13
78 6 0.05
79 9 0.08
80 23 0.20
81 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.47
Consensus pattern (80 bp):
AATTTAATTTATTTGGTTGCTTTTGAATATTATTAAATTCACATTTTTGTTTTATGGGATCAAAA
ATTAAATTAAGTTCG
Found at i:1469962 original size:152 final size:152
Alignment explanation
Indices: 1469763--1470067 Score: 610
Period size: 152 Copynumber: 2.0 Consensus size: 152
1469753 TAGCTTTAAG
1469763 ATCTGGTCTCGATATTTGTAAATAATCGAACATTCTTTATCTTTCTAAAACGACTTGGTAATTTT
1 ATCTGGTCTCGATATTTGTAAATAATCGAACATTCTTTATCTTTCTAAAACGACTTGGTAATTTT
1469828 AATTTAATTTATTTGGTTGCTTTTGAATATTATTAAATTCACATTTTTGTTTTATGGGATCAAAA
66 AATTTAATTTATTTGGTTGCTTTTGAATATTATTAAATTCACATTTTTGTTTTATGGGATCAAAA
1469893 ATTAAATTAAGTTCGAATTTAT
131 ATTAAATTAAGTTCGAATTTAT
1469915 ATCTGGTCTCGATATTTGTAAATAATCGAACATTCTTTATCTTTCTAAAACGACTTGGTAATTTT
1 ATCTGGTCTCGATATTTGTAAATAATCGAACATTCTTTATCTTTCTAAAACGACTTGGTAATTTT
1469980 AATTTAATTTATTTGGTTGCTTTTGAATATTATTAAATTCACATTTTTGTTTTATGGGATCAAAA
66 AATTTAATTTATTTGGTTGCTTTTGAATATTATTAAATTCACATTTTTGTTTTATGGGATCAAAA
1470045 ATTAAATTAAGTTCGAATTTAT
131 ATTAAATTAAGTTCGAATTTAT
1470067 A
1 A
1470068 AAGTTAATTG
Statistics
Matches: 153, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
152 153 1.00
ACGTcount: A:0.32, C:0.10, G:0.12, T:0.47
Consensus pattern (152 bp):
ATCTGGTCTCGATATTTGTAAATAATCGAACATTCTTTATCTTTCTAAAACGACTTGGTAATTTT
AATTTAATTTATTTGGTTGCTTTTGAATATTATTAAATTCACATTTTTGTTTTATGGGATCAAAA
ATTAAATTAAGTTCGAATTTAT
Found at i:1470413 original size:43 final size:43
Alignment explanation
Indices: 1470365--1470456 Score: 184
Period size: 43 Copynumber: 2.1 Consensus size: 43
1470355 TTTTAAATTA
1470365 AAAATCAATTGAAAGAGGATAATTAAGAATTAATGTGGTTTTT
1 AAAATCAATTGAAAGAGGATAATTAAGAATTAATGTGGTTTTT
1470408 AAAATCAATTGAAAGAGGATAATTAAGAATTAATGTGGTTTTT
1 AAAATCAATTGAAAGAGGATAATTAAGAATTAATGTGGTTTTT
1470451 AAAATC
1 AAAATC
1470457 TCACATTTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 49 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (43 bp):
AAAATCAATTGAAAGAGGATAATTAAGAATTAATGTGGTTTTT
Found at i:1471783 original size:6 final size:6
Alignment explanation
Indices: 1471772--1471807 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
1471762 TAACACCTTG
* *
1471772 TGCATT TGCATT TGCATT CGCATT CGCATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT TGCATT
1471808 CTTATTAGCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (6 bp):
TGCATT
Found at i:1471800 original size:18 final size:18
Alignment explanation
Indices: 1471773--1471808 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
1471763 AACACCTTGT
*
1471773 GCATTTGCATTTGCATTC
1 GCATTCGCATTTGCATTC
1471791 GCATTCGCATTTGCATTC
1 GCATTCGCATTTGCATTC
1471809 TTATTAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.42
Consensus pattern (18 bp):
GCATTCGCATTTGCATTC
Found at i:1472232 original size:84 final size:80
Alignment explanation
Indices: 1472132--1472297 Score: 296
Period size: 84 Copynumber: 2.0 Consensus size: 80
1472122 ATGTCCAAAA
1472132 TGATGGATAGAATAGATGCTTTGTCCAAAGGAAAAGAGACTTCTACCAAAGAAAAGAAAGAGCTC
1 TGATGGATAGAATAGATGCTTTGTCCAAAGG-AAAGAGACTTCTACC-AAGAAAAGAAAGAGCTC
1472197 GATGAAAACAATCTTGAGG
64 GATG--AACAATCTTGAGG
1472216 TGATGGATAGAATAGATGCTTTGTCCAAAGGAAAGAGACTTCTACCAAGAAAAGAAAGAGCTCGA
1 TGATGGATAGAATAGATGCTTTGTCCAAAGGAAAGAGACTTCTACCAAGAAAAGAAAGAGCTCGA
1472281 TGAACAATCTTGAGG
66 TGAACAATCTTGAGG
1472296 TG
1 TG
1472298 TCAAATACAC
Statistics
Matches: 82, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
80 15 0.18
82 21 0.26
83 15 0.18
84 31 0.38
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (80 bp):
TGATGGATAGAATAGATGCTTTGTCCAAAGGAAAGAGACTTCTACCAAGAAAAGAAAGAGCTCGA
TGAACAATCTTGAGG
Found at i:1476525 original size:16 final size:18
Alignment explanation
Indices: 1476493--1476527 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1476483 ATATAAAAAC
1476493 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
1476511 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
1476527 A
1 A
1476528 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:1477151 original size:37 final size:36
Alignment explanation
Indices: 1477108--1477209 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
1477098 ATAGTAGAAC
1477108 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
1477145 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
1477179 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1477210 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1479376 original size:42 final size:42
Alignment explanation
Indices: 1479313--1479412 Score: 132
Period size: 42 Copynumber: 2.4 Consensus size: 42
1479303 ATCAGTAAGT
* *
1479313 GCCATCAGTAA-CTCTTTCGAGCATGATGATGAAGTCCTTTGG
1 GCCATCAGTAAGC-CTTCCGAGCATGATGATGAAGTCCTTCGG
* *
1479355 GCTATCAGTAAGCCTTCCGAGCATGATGATTAAGTCCTTCGG
1 GCCATCAGTAAGCCTTCCGAGCATGATGATGAAGTCCTTCGG
*
1479397 GCCATC-TTAAGCCTTC
1 GCCATCAGTAAGCCTTC
1479413 ACGGAAGAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
41 9 0.18
42 41 0.80
43 1 0.02
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (42 bp):
GCCATCAGTAAGCCTTCCGAGCATGATGATGAAGTCCTTCGG
Found at i:1479393 original size:23 final size:23
Alignment explanation
Indices: 1479330--1479394 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 23
1479320 GTAACTCTTT
*
1479330 CGAGCATGATGATGAAGTCCTT-
1 CGAGCATGATGATTAAGTCCTTC
* * * *
1479352 TGGGC-T-ATCAGTAAG-CCTTC
1 CGAGCATGATGATTAAGTCCTTC
1479372 CGAGCATGATGATTAAGTCCTTC
1 CGAGCATGATGATTAAGTCCTTC
1479395 GGGCCATCTT
Statistics
Matches: 30, Mismatches: 9, Indels: 7
0.65 0.20 0.15
Matches are distributed among these distances:
19 4 0.13
20 9 0.30
21 2 0.07
22 10 0.33
23 5 0.17
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.29
Consensus pattern (23 bp):
CGAGCATGATGATTAAGTCCTTC
Found at i:1482623 original size:2 final size:2
Alignment explanation
Indices: 1482616--1482650 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1482606 TATTCCAAAA
1482616 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 A
1482651 GTGGTGTTTT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1482860 original size:108 final size:105
Alignment explanation
Indices: 1482632--1482834 Score: 235
Period size: 108 Copynumber: 1.9 Consensus size: 105
1482622 ATATATATAT
* * * ** * *
1482632 ATATATATATATATATATAGTGGTGTTTTTTCAATAAACGTCACTATAGATTGATATATTGCGAC
1 ATATATCTAAATATATATAGTGGTGTTTTTCCAATAAACACCACTATAGATAGACATATTGCGAC
1482697 GTTGTTTTATAAAAACGCCACTATTATTGCGCTGCCCAAAA
66 GTTGTTTTATAAAAACGCCACTATTATTGCGC-GCCCAAAA
* ** * *
1482738 AAATGCCAAAAAATATATATAGTGGTGTTTTTCCAATAAACACCACTATAGATAGACCTATTGCG
1 ATATATC--TAAATATATATAGTGGTGTTTTTCCAATAAACACCACTATAGATAGACATATTGCG
* *
1482803 ACGTTTTTTTTTCATAAAACGCCACTATTATT
64 ACGTTGTTTTAT-A-AAAACGCCACTATTATT
1482835 TCCCCGAAAT
Statistics
Matches: 79, Mismatches: 14, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
106 3 0.04
108 58 0.73
109 1 0.01
110 17 0.22
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.36
Consensus pattern (105 bp):
ATATATCTAAATATATATAGTGGTGTTTTTCCAATAAACACCACTATAGATAGACATATTGCGAC
GTTGTTTTATAAAAACGCCACTATTATTGCGCGCCCAAAA
Found at i:1484126 original size:27 final size:27
Alignment explanation
Indices: 1484085--1484177 Score: 132
Period size: 27 Copynumber: 3.4 Consensus size: 27
1484075 GATAATATCT
* *
1484085 CTGAATCATTTAAAATATACTTCTGTG
1 CTGAATCATTCAAAATGTACTTCTGTG
*
1484112 TTGAATCATTCAAAATGTACTTCTGTG
1 CTGAATCATTCAAAATGTACTTCTGTG
* * *
1484139 CTAAATCATTCAGAGTGTACTTCTGTG
1 CTGAATCATTCAAAATGTACTTCTGTG
1484166 CTGAATCATTCA
1 CTGAATCATTCA
1484178 GTACTATTTT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 58 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (27 bp):
CTGAATCATTCAAAATGTACTTCTGTG
Found at i:1484741 original size:18 final size:18
Alignment explanation
Indices: 1484718--1484763 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
1484708 TTCAAACCCT
*
1484718 TCACAACAATCTTCATCA
1 TCACAACAACCTTCATCA
1484736 TCACAACAACCTTCATCA
1 TCACAACAACCTTCATCA
1484754 TCACAACAAC
1 TCACAACAAC
1484764 AAGCTCAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (18 bp):
TCACAACAACCTTCATCA
Found at i:1496033 original size:22 final size:24
Alignment explanation
Indices: 1495989--1496035 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
1495979 ATGTGTTTAA
1495989 TTTATGATTATAATTATAAATATTT
1 TTTATGATTATAA-TATAAATATTT
*
1496014 TTTATGATT-TAAATATATATAT
1 TTTATGATTAT-AATATAAATAT
1496036 GTAAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
TTTATGATTATAATATAAATATTT
Found at i:1496035 original size:24 final size:25
Alignment explanation
Indices: 1495989--1496035 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1495979 ATGTGTTTAA
*
1495989 TTTATGATTATAATTATAAATATTT
1 TTTATGATTATAAATATAAATATTT
*
1496014 TTTATGATT-TAAATATATATAT
1 TTTATGATTATAAATATAAATAT
1496036 GTAAATTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
TTTATGATTATAAATATAAATATTT
Found at i:1496072 original size:2 final size:2
Alignment explanation
Indices: 1496061--1496096 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
1496051 TAGCTACTTC
1496061 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1496097 ATTTGAACGT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1504226 original size:16 final size:16
Alignment explanation
Indices: 1504178--1504234 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
1504168 ACATTTTAAG
*
1504178 TCTAAAATAAGATAAA
1 TCTAAAATAATATAAA
**
1504194 TAAAAAATAAT-TCAAA
1 TCTAAAATAATAT-AAA
1504210 TCTAAAATAATATAAA
1 TCTAAAATAATATAAA
1504226 TTCTAAAAT
1 -TCTAAAAT
1504235 GATACCATCC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
15 1 0.03
16 23 0.70
17 9 0.27
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (16 bp):
TCTAAAATAATATAAA
Found at i:1504848 original size:30 final size:31
Alignment explanation
Indices: 1504798--1504898 Score: 107
Period size: 31 Copynumber: 3.3 Consensus size: 31
1504788 GAATGAATTT
* * *
1504798 TTAATTTAACTCTTGAATTTTAGATGGAATA
1 TTAATTTGACTCTTAAATTTTAGATAGAATA
* *
1504829 CTAATTTGA-TCTTAAATTTTATA-AGATATA
1 TTAATTTGACTCTTAAATTTTAGATAGA-ATA
* * *
1504859 TTATTTTGACTCTTAAACTTTAGATAAAATA
1 TTAATTTGACTCTTAAATTTTAGATAGAATA
1504890 TTAATTTGA
1 TTAATTTGA
1504899 TCACTGAATT
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
29 2 0.04
30 22 0.39
31 30 0.54
32 2 0.04
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.47
Consensus pattern (31 bp):
TTAATTTGACTCTTAAATTTTAGATAGAATA
Found at i:1510809 original size:27 final size:26
Alignment explanation
Indices: 1510756--1510832 Score: 75
Period size: 27 Copynumber: 2.8 Consensus size: 26
1510746 ATATATTTTA
*
1510756 ATAATATAAAACTTTAAAATAAAATAACT
1 ATAA-ATAAAA-TTTAAAA-AAAATAAAT
*
1510785 ATAAATAAAATTTAAAAAATTATAAAT
1 ATAAATAAAATTTAAAAAA-AATAAAT
*
1510812 A-AAATAAATAATTAAAAAAAA
1 ATAAATAAA-ATTTAAAAAAAA
1510833 AGTAAATTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
26 10 0.24
27 22 0.52
28 6 0.14
29 4 0.10
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (26 bp):
ATAAATAAAATTTAAAAAAAATAAAT
Found at i:1510810 original size:21 final size:22
Alignment explanation
Indices: 1510775--1510816 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1510765 AACTTTAAAA
1510775 TAAAATAACTATAAATAAAATT
1 TAAAATAACTATAAATAAAATT
*
1510797 TAAAA-AATTATAAATAAAAT
1 TAAAATAACTATAAATAAAAT
1510817 AAATAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAACTATAAATAAAATT
Found at i:1525446 original size:19 final size:19
Alignment explanation
Indices: 1525418--1525465 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
1525408 TGAATCATAT
1525418 TTTTACTTTTCATT-TCTTA
1 TTTTACTTTTCATTAT-TTA
* *
1525437 TTTTAGTTTTTATTATTTA
1 TTTTACTTTTCATTATTTA
1525456 TTTTTACTTT
1 -TTTTACTTT
1525466 ACATGTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTACTTTTCATTATTTA
Found at i:1528269 original size:3 final size:3
Alignment explanation
Indices: 1528261--1528337 Score: 91
Period size: 3 Copynumber: 24.7 Consensus size: 3
1528251 TTTTTCATAC
* * * *
1528261 TAT TAT TAT TAT TTT TAT TAT TTT TAT TAT TAT TAT CAT ACAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT
1528307 TAT TAAT TAT TAAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT T-AT TAT TAT TAT TAT TAT TA
1528338 AATAAATATA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
3 56 0.86
4 9 0.14
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1528317 original size:7 final size:7
Alignment explanation
Indices: 1528305--1528338 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
1528295 ATCATACATT
1528305 ATTATTA
1 ATTATTA
1528312 ATTATTA
1 ATTATTA
1528319 ATTATT-
1 ATTATTA
1528325 ATTATT-
1 ATTATTA
1528331 ATTATTA
1 ATTATTA
1528338 A
1 A
1528339 ATAAATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.46
7 14 0.54
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (7 bp):
ATTATTA
Found at i:1532217 original size:55 final size:55
Alignment explanation
Indices: 1532075--1532252 Score: 221
Period size: 55 Copynumber: 3.2 Consensus size: 55
1532065 CAGCGTATTT
* * * * *
1532075 GCTCCTTATTCTTTTCAGGGAGTATAGAATTCTATAAATCTTCAGAAAAATGGGTTC
1 GCTCCCTATTC-TTTCAGGGAGTATAGAACTCAAGAAATCTTCAG-AAAACGGGTTC
* * * *
1532132 GCTCCCTATTTCTTTCAGGGAGTATAGAACTCGAGAAATCTTCAGCAAACGTGTCC
1 GCTCCCTA-TTCTTTCAGGGAGTATAGAACTCAAGAAATCTTCAGAAAACGGGTTC
* * *
1532188 GCTCCCTATTCTTTCAGGGAGTGTAGAACTCAAGAAATCTTCTGAAAACGGGTTT
1 GCTCCCTATTCTTTCAGGGAGTATAGAACTCAAGAAATCTTCAGAAAACGGGTTC
1532243 GCTCCCTATT
1 GCTCCCTATT
1532253 ATTCTGAGAA
Statistics
Matches: 105, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
55 50 0.48
56 15 0.14
57 37 0.35
58 3 0.03
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (55 bp):
GCTCCCTATTCTTTCAGGGAGTATAGAACTCAAGAAATCTTCAGAAAACGGGTTC
Found at i:1532418 original size:42 final size:41
Alignment explanation
Indices: 1532326--1532422 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
1532316 AGGTCTTATG
* * *
1532326 GATGACCCGAAGGATTTATCATCTTGCTCGAGAGACTCACA
1 GATGACCCGAAGGATTTAACATCATGCTCGAAAGACTCACA
* * *
1532367 AATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGATTT-AACATCATGCTCGAAAGACTCACA
*
1532409 GATGGCCCGAAGGA
1 GATGACCCGAAGGA
1532423 CTTATAAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 16 0.34
42 31 0.66
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.22
Consensus pattern (41 bp):
GATGACCCGAAGGATTTAACATCATGCTCGAAAGACTCACA
Found at i:1532815 original size:219 final size:214
Alignment explanation
Indices: 1532300--1533062 Score: 1195
Period size: 219 Copynumber: 3.5 Consensus size: 214
1532290 ACCTTGGTGC
* * * * * * *
1532300 AAAACATCCTGCCCGAAGGTCTTATGGATGACCCGAAGGATTTATCATCTTGCTCGAGAGACTCA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* *
1532365 CAAATGACCCGAAGGATTTAAACATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* *
1532430 ATTGTGAAATTTTGAAATCGCATTCTTCCTTTTCAAAAATTCCATCTTCTTAAAACATCA-TTTT
131 ATTGTGAAATTTTAAAATCGCATTCTTCATTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
* *
1532494 CTCATTTTCAAATTCATTTG
196 TTCATTTTCAAATTCA-TGG
* *
1532514 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCAAAGGATTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
* * *
1532579 CAGGTGACCCTAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAAGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
*
1532644 ATTGTGAAATTTTAAAAATCGCATTCTTCGTTTTCAAAAATTCCATCTTCTTAAAACATCATCAT
131 ATTGTGAAATTTT-AAAATCGCATTCTTCATTTTCAAAAATTCCATCTTCTT-AAA-A-CATCA-
*
1532709 TTTTTTTTATTTTCAAATTCATGG
191 TTTTTTTCATTTTCAAATTCATGG
*
1532733 AAAACACCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
*
1532798 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGACCCGAAGGACTTATAA
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
* * *
1532863 ATTGTCAAATTTTGAAAATCGCATTATTCATTTTCAAAAATTTCATCTTCTTAAAACATCATTTT
131 ATTGTGAAATTTT-AAAATCGCATTCTTCATTTTCAAAAATTCCATCTTCTTAAAACATCATTTT
*
1532928 TTTCATTTCCAAATTCATGTG
195 TTTCATTTTCAAATTCATG-G
* *
1532949 AAAATATCCTACCCGAAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1 AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
1533014 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
66 CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGG
1533063 GTTTGCTTCA
Statistics
Matches: 507, Mismatches: 35, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
214 131 0.26
215 57 0.11
216 119 0.23
217 2 0.00
218 8 0.02
219 172 0.34
220 18 0.04
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (214 bp):
AAAACATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTA
CAGATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAA
ATTGTGAAATTTTAAAATCGCATTCTTCATTTTCAAAAATTCCATCTTCTTAAAACATCATTTTT
TTCATTTTCAAATTCATGG
Found at i:1532840 original size:42 final size:41
Alignment explanation
Indices: 1532759--1532859 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 41
1532749 AGGTCTTATG
* * * * *
1532759 GATGGCCCGAAGGACTTATCATCTTGCTCTAAAGGCTTACA
1 GATGACCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
* *
1532800 GATGACCCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGACCCGAAGGACTT-AGCATCATGCTCGAAAGACTTACA
1532842 GATGACCCGAAGGACTTA
1 GATGACCCGAAGGACTTA
1532860 TAAATTGTCA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
41 16 0.31
42 35 0.69
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (41 bp):
GATGACCCGAAGGACTTAGCATCATGCTCGAAAGACTTACA
Found at i:1532857 original size:20 final size:20
Alignment explanation
Indices: 1532790--1532859 Score: 54
Period size: 20 Copynumber: 3.5 Consensus size: 20
1532780 TCTTGCTCTA
*
1532790 AAGG-CTTACAGATGACCCG
1 AAGGACTTACTGATGACCCG
* * *
1532809 AAGGATTTAAGCATCATG-CTCG
1 AAGGACTT-A-C-TGATGACCCG
*
1532831 AAAGACTTACTGATGACCCG
1 AAGGACTTACTGATGACCCG
1532851 AAGGACTTA
1 AAGGACTTA
1532860 TAAATTGTCA
Statistics
Matches: 37, Mismatches: 9, Indels: 9
0.67 0.16 0.16
Matches are distributed among these distances:
19 8 0.22
20 14 0.38
21 2 0.05
22 10 0.27
23 3 0.08
ACGTcount: A:0.34, C:0.21, G:0.23, T:0.21
Consensus pattern (20 bp):
AAGGACTTACTGATGACCCG
Found at i:1533158 original size:37 final size:38
Alignment explanation
Indices: 1533100--1533252 Score: 224
Period size: 37 Copynumber: 4.1 Consensus size: 38
1533090 CTTAAGGTGG
* * *
1533100 TGCTTCACTAC-TCTTCGGTGAAGGTTTAAGATTGATT
1 TGCTTCACTCCTTCTTCAGTGAAGGCTTAAGATTGATT
1533137 TGCTTCACTCCTTCTT-AGTGAAGGCTTAAGATTGATT
1 TGCTTCACTCCTTCTTCAGTGAAGGCTTAAGATTGATT
1533174 TGCTTCACTCCTTCTT-AGTGAAGGCTTAAGATTGATT
1 TGCTTCACTCCTTCTTCAGTGAAGGCTTAAGATTGATT
* *
1533211 TGCTTCCCTCCTT-TTCGGTGAAGGCTTAAGATTGACTT
1 TGCTTCACTCCTTCTTCAGTGAAGGCTTAAGATTGA-TT
1533249 TGCT
1 TGCT
1533253 CCAATCTCAT
Statistics
Matches: 108, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
36 2 0.02
37 96 0.89
38 10 0.09
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.41
Consensus pattern (38 bp):
TGCTTCACTCCTTCTTCAGTGAAGGCTTAAGATTGATT
Found at i:1539236 original size:20 final size:20
Alignment explanation
Indices: 1539213--1539263 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1539203 AAATTAATAA
*
1539213 GCAATTGCAAAAATAAGAAT
1 GCAAATGCAAAAATAAGAAT
1539233 GCAAATGCAAAAATAAGAAT
1 GCAAATGCAAAAATAAGAAT
1539253 GCAAATGCAAA
1 GCAAATGCAAA
1539264 TGCACGAGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.57, C:0.12, G:0.16, T:0.16
Consensus pattern (20 bp):
GCAAATGCAAAAATAAGAAT
Found at i:1539978 original size:49 final size:49
Alignment explanation
Indices: 1539883--1539979 Score: 117
Period size: 49 Copynumber: 2.0 Consensus size: 49
1539873 TCATTAACAA
*
1539883 AAAATCCTAACCGCATGGTATCTAATTCACATACTTTGTGCGAAAATAT
1 AAAATCCTAACCGCATGGTATCTAATTCACATACTTTGTGCAAAAATAT
* * * *
1539932 AAAA-CCTAACCGCATGCTTTTCTAGTTCTCATACTTCT-TGCAAAAATA
1 AAAATCCTAACCGCATG-GTATCTAATTCACATACTT-TGTGCAAAAATA
1539980 AATTCGAGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 12 0.29
49 28 0.68
50 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (49 bp):
AAAATCCTAACCGCATGGTATCTAATTCACATACTTTGTGCAAAAATAT
Found at i:1543594 original size:19 final size:19
Alignment explanation
Indices: 1543542--1543587 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1543532 GTCAACCACC
*
1543542 CCACGTTGACACCTCACTA
1 CCACGTCGACACCTCACTA
1543561 CCACGTCGACACCTCACTA
1 CCACGTCGACACCTCACTA
1543580 CCACGTCG
1 CCACGTCG
1543588 CAGCCTCTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.46, G:0.13, T:0.17
Consensus pattern (19 bp):
CCACGTCGACACCTCACTA
Found at i:1552505 original size:24 final size:24
Alignment explanation
Indices: 1552478--1552565 Score: 149
Period size: 24 Copynumber: 3.7 Consensus size: 24
1552468 TTCTATTATA
1552478 ATACCTGACCTGGATTCTGATCGG
1 ATACCTGACCTGGATTCTGATCGG
* *
1552502 ATACTTGACCTGGATTCTGATCGA
1 ATACCTGACCTGGATTCTGATCGG
*
1552526 ATACCTGACCTAGATTCTGATCGG
1 ATACCTGACCTGGATTCTGATCGG
1552550 ATACCTGACCTGGATT
1 ATACCTGACCTGGATT
1552566 ATGTTTTGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (24 bp):
ATACCTGACCTGGATTCTGATCGG
Found at i:1552696 original size:35 final size:35
Alignment explanation
Indices: 1552646--1552746 Score: 193
Period size: 35 Copynumber: 2.9 Consensus size: 35
1552636 TATACCTGGA
*
1552646 GGCTCCTCGGTTGTGTGCTCAGGGCCTTACTTACC
1 GGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
1552681 GGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
1 GGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
1552716 GGCTCCTCGGCTGTGTGCTCAGGGCCTTACT
1 GGCTCCTCGGCTGTGTGCTCAGGGCCTTACT
1552747 GGATTTGACG
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.08, C:0.33, G:0.30, T:0.30
Consensus pattern (35 bp):
GGCTCCTCGGCTGTGTGCTCAGGGCCTTACTTACC
Found at i:1555842 original size:24 final size:24
Alignment explanation
Indices: 1555815--1555898 Score: 123
Period size: 24 Copynumber: 3.5 Consensus size: 24
1555805 TTCTATTATA
* *
1555815 ATACCTGACTTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
*
1555839 ATACTTGACCTGGATTCTGATCGA
1 ATACTTGACCTGGATTCTGATCGG
* *
1555863 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
1555887 ATACTTGACCTG
1 ATACTTGACCTG
1555899 AATTATGTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 54 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:1558537 original size:23 final size:23
Alignment explanation
Indices: 1558501--1558563 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
1558491 ATGAAGACCA
1558501 TGCTGAATGATTCAACAAAACAC
1 TGCTGAATGATTCAACAAAACAC
* * *
1558524 TGTTGTATGATTCAACAAAACGC
1 TGCTGAATGATTCAACAAAACAC
1558547 TGCTGAATGATTCAACA
1 TGCTGAATGATTCAACA
1558564 TTAAAGTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.27
Consensus pattern (23 bp):
TGCTGAATGATTCAACAAAACAC
Found at i:1558652 original size:18 final size:17
Alignment explanation
Indices: 1558626--1558667 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
1558616 CAGAGCTAAT
*
1558626 TCATACAGAGCATTTGAA
1 TCATTCAGAGCA-TTGAA
*
1558644 TCATTCAGATCATTGAA
1 TCATTCAGAGCATTGAA
1558661 TCATTCA
1 TCATTCA
1558668 ACGTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (17 bp):
TCATTCAGAGCATTGAA
Found at i:1563028 original size:16 final size:16
Alignment explanation
Indices: 1563007--1563059 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
1562997 TAGACACTTA
*
1563007 TTTTTATCCATATATT
1 TTTTTATACATATATT
*
1563023 TTTTTATACATATATA
1 TTTTTATACATATATT
* * *
1563039 TCTATATA-ATATATA
1 TTTTTATACATATATT
1563054 TTTTTA
1 TTTTTA
1563060 AAACATTTTG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
15 11 0.35
16 20 0.65
ACGTcount: A:0.34, C:0.08, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTTATACATATATT
Found at i:1564522 original size:34 final size:34
Alignment explanation
Indices: 1564457--1564521 Score: 91
Period size: 33 Copynumber: 1.9 Consensus size: 34
1564447 TTTGTCCCCA
1564457 TTATTATTGATATATATATTTTATTATTTTTTCC
1 TTATTATTGATATATATATTTTATTATTTTTTCC
1564491 TTATTATT-ATAT-T-TATTGTTATATATTTTTT
1 TTATTATTGATATATATATT-TTAT-TATTTTTT
1564522 TATCTTATCA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
31 4 0.14
32 5 0.17
33 12 0.41
34 8 0.28
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (34 bp):
TTATTATTGATATATATATTTTATTATTTTTTCC
Found at i:1564628 original size:3 final size:3
Alignment explanation
Indices: 1564620--1564684 Score: 103
Period size: 3 Copynumber: 20.7 Consensus size: 3
1564610 TTTCTGTTTG
1564620 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1564668 TATA TATA TATA TTA TT
1 T-TA T-TA T-TA TTA TT
1564685 TCTTTTTTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 50 0.82
4 11 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1564696 original size:15 final size:15
Alignment explanation
Indices: 1564678--1564707 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1564668 TATATATATA
1564678 TATTATTTCTTTTTT
1 TATTATTTCTTTTTT
*
1564693 TATTATTTGTTTTTT
1 TATTATTTCTTTTTT
1564708 ACACAACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.03, G:0.03, T:0.80
Consensus pattern (15 bp):
TATTATTTCTTTTTT
Found at i:1572222 original size:21 final size:21
Alignment explanation
Indices: 1572196--1572238 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1572186 CGAAAGTTAC
1572196 TGTAGCAGTGTATCGATGCAT
1 TGTAGCAGTGTATCGATGCAT
1572217 TGTAGCAGTGTATCGATGCAT
1 TGTAGCAGTGTATCGATGCAT
1572238 T
1 T
1572239 ATTGATATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (21 bp):
TGTAGCAGTGTATCGATGCAT
Found at i:1572287 original size:44 final size:44
Alignment explanation
Indices: 1572217--1572303 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
1572207 ATCGATGCAT
* * **
1572217 TGTAGCAGTGTATCGATGCATTATTGATATTCGAAAGTTTTCAC
1 TGTAGCAGTGCATCGATACACAATTGATATTCGAAAGTTTTCAC
1572261 TGTAGCAGTGCATCGATACACAATTGATATTCGAAAGTTTTCA
1 TGTAGCAGTGCATCGATACACAATTGATATTCGAAAGTTTTCA
1572304 TTGTTCATTA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.36
Consensus pattern (44 bp):
TGTAGCAGTGCATCGATACACAATTGATATTCGAAAGTTTTCAC
Found at i:1573890 original size:24 final size:24
Alignment explanation
Indices: 1573855--1573903 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
1573845 TTCTTTGGTG
1573855 GATCAGAATGTTGCCAAGTTAGTT
1 GATCAGAATGTTGCCAAGTTAGTT
*
1573879 GATCAGATTGTTGCCAAGTTAGTT
1 GATCAGAATGTTGCCAAGTTAGTT
1573903 G
1 G
1573904 GCCTATATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.35
Consensus pattern (24 bp):
GATCAGAATGTTGCCAAGTTAGTT
Found at i:1577012 original size:84 final size:84
Alignment explanation
Indices: 1576808--1578141 Score: 1501
Period size: 84 Copynumber: 15.9 Consensus size: 84
1576798 AAAGCACATT
* * * * * *
1576808 CAACAAAAGACCTTCGAGTTTGATTACACTCAACTCAAAGACACATCATTTACAACATAACTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
1576873 GGCGAGAAGGGTTATCTGT
66 GGCGAGAAGGGTTATCTGC
* * * * * *
1576892 CAAC-CAAGACCTTTGAGTTCGATTACACTCAGCTCAAATGCACATCATTTGTAGCATAACTTAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * *
1576956 GACGAGAAGGGATATATGC
66 GGCGAGAAGGGTTATCTGC
* * * * *
1576975 CAACAAAAGACCTTCGAGTTCGATTACAGTTAGCTCAAAGGCACATTATTTGCAGCATAACTCAT
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * * **
1577040 GGCAAGAAGGGCTGTCTAT
66 GGCGAGAAGGGTTATCTGC
* * * * * * **
1577059 TAACAAAAGACCTTCGAGTTCGATTACATTCAGCTAAAAGGCATATCCAATTTACAGTATAAATC
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACAT-C-ATTTGCAGCATAGCTC
* *
1577124 AAAGCGAGAAGGGTTATCTGT
64 AAGGCGAGAAGGGTTATCTGC
* * * * * *
1577145 TAAC-CAATACCTTCGAGTTTGATTACACTAAGCTCAAAAGCACATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
1577209 GGTGAGAGGGGTTATCTGC
66 GGCGAGAAGGGTTATCTGC
* * * * *
1577228 CAGCAAAAGACCTTCAAGTTCAATTACACTCAGCTTAAAGGCACATCATTTGCAGCAGAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * *
1577293 GGTGAGAAGGGCTATCTAC
66 GGCGAGAAGGGTTATCTGC
* * *
1577312 CAATAAAATACCTTCGAGTTC-ATTTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCA
1 CAACAAAAGACCTTCGAGTTCGA-TTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
1577376 AGGCGAGAAGGGTTATCTGC
65 AGGCGAGAAGGGTTATCTGC
* * * * * *
1577396 CAACAGAAGACCTTTGAGTTTGATTACACTTAACTCAAAGGCACATCATTTGCAACATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
1577461 CGCGAGAAGGGTTATCTGC
66 GGCGAGAAGGGTTATCTGC
** * * * *
1577480 CAACAAAAGACCTTTAATTTTGATTACACTCAGCTCAAAGGCACATCATTTGTAGCATATCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* *
1577545 AGCGAGAAGGGCTATCTGC
66 GGCGAGAAGGGTTATCTGC
*
1577564 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTACAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
** *
1577629 GGCGAGAA-TATATATCTAC
66 GGCGAGAAGGGT-TATCTGC
* * *
1577648 CAATAAAAGACCTTCGATTTTGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * *
1577713 GGTGAGAAGGGCTATCTGT
66 GGCGAGAAGGGTTATCTGC
* **
1577732 CAACAAAAG-GCTTCCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTAAAGCATAGCTCA
1 CAACAAAAGACCTT-CGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCA
** *
1577796 AGGCGAGAA-TATATATCTAC
65 AGGCGAGAAGGGT-TATCTGC
* * * * * *
1577816 CAATAAAAGACCTTCGATTTTGATTACACTCAGCTCAAAGGCACATCATTTACAGAATAGCTAAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
1577881 GGCGAGAAGGGCTATCTGC
66 GGCGAGAAGGGTTATCTGC
* * * ** *
1577900 CAACAAAAGACCTTCGAGTTTGATTACACTTAGCTTAAAGGCACATCATTTGCAATATAGCTCGA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
1577965 GGTGAGAATGGGTTATCTGC
66 GGCGAGAA-GGGTTATCTGC
* ** * *
1577985 CAACAAAAGACCTTCGAGCTCGATTACACTCAGCTCAAAGGCACATCATTTGCAAAATAACTTAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
* * ** * * *
1578050 GTCGAAAAAAGATATATGT
66 GGCGAGAAGGGTTATCTGC
* * * * *
1578069 TAACAAAAGACCTTCGAGTTCGATTACACTCAGTTCAAAGGCACATAATTTGCAACATAGCTTAA
1 CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
*
1578134 GTCGAGAA
66 GGCGAGAA
1578142 AATTTATCTG
Statistics
Matches: 1055, Mismatches: 182, Indels: 26
0.84 0.14 0.02
Matches are distributed among these distances:
83 104 0.10
84 810 0.77
85 109 0.10
86 32 0.03
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (84 bp):
CAACAAAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAGCTCAA
GGCGAGAAGGGTTATCTGC
Found at i:1578773 original size:19 final size:20
Alignment explanation
Indices: 1578751--1578798 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1578741 GTTTTTGAAA
1578751 ATATTTTTAT-ATATATAAT
1 ATATTTTTATCATATATAAT
* * *
1578770 ATATTGTTATCATTTATTAT
1 ATATTTTTATCATATATAAT
1578790 -TATTTTTAT
1 ATATTTTTAT
1578799 TTATTTATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
ATATTTTTATCATATATAAT
Found at i:1580195 original size:19 final size:18
Alignment explanation
Indices: 1580126--1580198 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 18
1580116 ATATTTATTG
1580126 TTATATATTTTTATTTATC
1 TTATATA-TTTTATTTATC
* *
1580145 TTATCTATTTTAGTTTTTCC
1 TTATATATTTTA-TTTAT-C
*
1580165 TTA-ATA-TTTATTTATA
1 TTATATATTTTATTTATC
1580181 TGTATATATTTTATTTAT
1 T-TATATATTTTATTTAT
1580199 TATCCTTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
16 1 0.02
17 6 0.14
18 12 0.27
19 21 0.48
20 4 0.09
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (18 bp):
TTATATATTTTATTTATC
Found at i:1580387 original size:21 final size:21
Alignment explanation
Indices: 1580363--1580402 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1580353 TTTTTTTCTA
1580363 TTTTT-CTATGTTTTTTATTCC
1 TTTTTCCT-TGTTTTTTATTCC
*
1580384 TTTTTCCTTTTTTTTTATT
1 TTTTTCCTTGTTTTTTATT
1580403 TTTGTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (21 bp):
TTTTTCCTTGTTTTTTATTCC
Found at i:1580405 original size:11 final size:11
Alignment explanation
Indices: 1580391--1580464 Score: 55
Period size: 11 Copynumber: 6.9 Consensus size: 11
1580381 TCCTTTTTCC
1580391 TTTTT-TTTTA
1 TTTTTGTTTTA
1580401 TTTTTGTTTTA
1 TTTTTGTTTTA
*
1580412 -TTTCGTTTTA
1 TTTTTGTTTTA
*
1580422 TTTTTATTTTAA
1 TTTTTGTTTT-A
** * *
1580434 CATTT-TATTG
1 TTTTTGTTTTA
*
1580444 GTTTTGTTTTA
1 TTTTTGTTTTA
1580455 TTTTTGTTTT
1 TTTTTGTTTT
1580465 TAGTCATTTT
Statistics
Matches: 48, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
10 17 0.35
11 27 0.56
12 4 0.08
ACGTcount: A:0.12, C:0.03, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTGTTTTA
Found at i:1580498 original size:21 final size:21
Alignment explanation
Indices: 1580458--1580498 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1580448 TGTTTTATTT
*
1580458 TTGTTTTTAGTCATTTTTTTG
1 TTGTTTTTAGTCATTGTTTTG
* *
1580479 TTGTTTTTATTTATTGTTTT
1 TTGTTTTTAGTCATTGTTTT
1580499 CATATTTATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.02, G:0.12, T:0.76
Consensus pattern (21 bp):
TTGTTTTTAGTCATTGTTTTG
Found at i:1581750 original size:2 final size:2
Alignment explanation
Indices: 1581743--1581776 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1581733 CTAAAAATGG
1581743 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
1581777 CGTCTTACTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1582362 original size:22 final size:22
Alignment explanation
Indices: 1582334--1582375 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1582324 ATAGTTGAAG
*
1582334 TTTTATATTGTCTCGTATAATC
1 TTTTATATTATCTCGTATAATC
1582356 TTTTATATTATCTCGTATAA
1 TTTTATATTATCTCGTATAA
1582376 GTGTTGGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.12, G:0.07, T:0.55
Consensus pattern (22 bp):
TTTTATATTATCTCGTATAATC
Found at i:1585268 original size:31 final size:31
Alignment explanation
Indices: 1585230--1585310 Score: 144
Period size: 31 Copynumber: 2.6 Consensus size: 31
1585220 AGGGTCGAGG
1585230 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
1585261 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
1585292 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
1585311 AATCTATGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1586031 original size:21 final size:21
Alignment explanation
Indices: 1586005--1586045 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1585995 GAATTTTTTG
*
1586005 TGCATCGATGCACTGTAGCAA
1 TGCATCGATGCACCGTAGCAA
*
1586026 TGCATCGATGTACCGTAGCA
1 TGCATCGATGCACCGTAGCA
1586046 CTGTTTATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.24, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCATCGATGCACCGTAGCAA
Found at i:1588262 original size:27 final size:26
Alignment explanation
Indices: 1588220--1588283 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
1588210 AGTCAACCCG
*
1588220 TTAACTTTGACAGTTGACTTTGACTCA
1 TTAACTTTGACAGTTGAATTTGAC-CA
** *
1588247 TTAACTTTGATTGTTGAATTTGACCG
1 TTAACTTTGACAGTTGAATTTGACCA
1588273 TTAACTTTGAC
1 TTAACTTTGAC
1588284 CAAAAATTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 11 0.34
27 21 0.66
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (26 bp):
TTAACTTTGACAGTTGAATTTGACCA
Found at i:1588284 original size:13 final size:13
Alignment explanation
Indices: 1588217--1588284 Score: 66
Period size: 13 Copynumber: 5.2 Consensus size: 13
1588207 CCGAGTCAAC
1588217 CCGTTAACTTTGA
1 CCGTTAACTTTGA
* *
1588230 CAGTTGACTTTGA
1 CCGTTAACTTTGA
*
1588243 CTCATTAACTTTGA
1 C-CGTTAACTTTGA
**
1588257 TTGTTGAA-TTTGA
1 CCGTT-AACTTTGA
1588270 CCGTTAACTTTGA
1 CCGTTAACTTTGA
1588283 CC
1 CC
1588285 AAAAATTTCA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
12 2 0.05
13 29 0.69
14 11 0.26
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (13 bp):
CCGTTAACTTTGA
Found at i:1595413 original size:29 final size:28
Alignment explanation
Indices: 1595371--1595432 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
1595361 CTTAATCAAT
* *
1595371 TCAACTCCCTTGAGTCAACCTGGACTGAG
1 TCAACTCACTTGAGTCAA-CTCGACTGAG
* *
1595400 TCAACTCATTTGAGTCAACTCGTCTGAG
1 TCAACTCACTTGAGTCAACTCGACTGAG
1595428 TCAAC
1 TCAAC
1595433 CTGTTGACTT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (28 bp):
TCAACTCACTTGAGTCAACTCGACTGAG
Found at i:1595415 original size:14 final size:14
Alignment explanation
Indices: 1595395--1595432 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1595385 TCAACCTGGA
1595395 CTGAGTCAACTCAT
1 CTGAGTCAACTCAT
* *
1595409 TTGAGTCAACTCGT
1 CTGAGTCAACTCAT
1595423 CTGAGTCAAC
1 CTGAGTCAAC
1595433 CTGTTGACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (14 bp):
CTGAGTCAACTCAT
Found at i:1597972 original size:13 final size:13
Alignment explanation
Indices: 1597954--1598005 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
1597944 GTCATAAATC
1597954 TATGACGCGCATT
1 TATGACGCGCATT
1597967 TATGACGCGCATT
1 TATGACGCGCATT
**
1597980 TATGACATGCATT
1 TATGACGCGCATT
*
1597993 TATGTCGCGCATT
1 TATGACGCGCATT
1598006 GAGCGTCATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (13 bp):
TATGACGCGCATT
Found at i:1598184 original size:17 final size:16
Alignment explanation
Indices: 1598162--1598193 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
1598152 TTTCGTAAAT
1598162 TATATAATATATATATA
1 TATATAATAT-TATATA
1598179 TATATAATATTATAT
1 TATATAATATTATAT
1598194 TGACAAATAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TATATAATATTATATA
Found at i:1599512 original size:45 final size:44
Alignment explanation
Indices: 1599405--1599539 Score: 216
Period size: 44 Copynumber: 3.0 Consensus size: 44
1599395 AGCTTCATGT
* * *
1599405 TATTCTTACTGAAATTATAATTGGTCTATAGCTTTATATTGCCA
1 TATTCTTACTGAAATTGTAATTGGTCTATGGCTTTATGTTGCCA
1599449 TATTCTTACTGAAATTGTAATTGGTCTATGGCTTTATGTTGCCGA
1 TATTCTTACTGAAATTGTAATTGGTCTATGGCTTTATGTTGCC-A
* *
1599494 TATTCTTACTGAAATTGTAATTGGTCTATGGCTATATGTTGGCA
1 TATTCTTACTGAAATTGTAATTGGTCTATGGCTTTATGTTGCCA
1599538 TA
1 TA
1599540 GATACTCCAT
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
44 43 0.51
45 42 0.49
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.44
Consensus pattern (44 bp):
TATTCTTACTGAAATTGTAATTGGTCTATGGCTTTATGTTGCCA
Found at i:1599571 original size:2 final size:2
Alignment explanation
Indices: 1599559--1599589 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
1599549 TATTTGGTGC
1599559 AT AT GAT 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
1599590 GTCGCCAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1599647 original size:59 final size:60
Alignment explanation
Indices: 1599583--1599701 Score: 231
Period size: 60 Copynumber: 2.0 Consensus size: 60
1599573 TATATATATA
1599583 TATATATGT-CGCCAAGTTGATAACAATAATGATAAATGAACATTACCGTACTGTTTTTC
1 TATATATGTCCGCCAAGTTGATAACAATAATGATAAATGAACATTACCGTACTGTTTTTC
1599642 TATATATGTCCGCCAAGTTGATAACAATAATGATAAATGAACATTACCGTACTGTTTTTC
1 TATATATGTCCGCCAAGTTGATAACAATAATGATAAATGAACATTACCGTACTGTTTTTC
1599702 AAAAGTTATA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
59 9 0.15
60 50 0.85
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (60 bp):
TATATATGTCCGCCAAGTTGATAACAATAATGATAAATGAACATTACCGTACTGTTTTTC
Found at i:1603112 original size:19 final size:19
Alignment explanation
Indices: 1603088--1603139 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1603078 AATGCAAATG
1603088 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGGA
1603107 GTGCATCGATGCATAAGGA
1 GTGCATCGATGCATAAGGA
1603126 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1603140 CCCTTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.29, C:0.17, G:0.31, T:0.23
Consensus pattern (19 bp):
GTGCATCGATGCATAAGGA
Found at i:1603236 original size:20 final size:22
Alignment explanation
Indices: 1603191--1603248 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1603181 GCATGGGTAG
1603191 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1603215 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
1603235 TGCATCGTTGCACT
1 TGCATCGATGCACT
1603249 TCAAGGGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1603874 original size:21 final size:21
Alignment explanation
Indices: 1603849--1603918 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
1603839 TGTGAACATG
1603849 TGAATTATATGAAAAGTGATA
1 TGAATTATATGAAAAGTGATA
* * **
1603870 TGAATTACATGTAAAGAAACTA
1 TGAATTATATGAAAAGTGA-TA
* *
1603892 TGAGCTTATATGAACATGTGATA
1 TGA-ATTATATGAA-AAGTGATA
1603915 TGAA
1 TGAA
1603919 AGTGTATATG
Statistics
Matches: 35, Mismatches: 11, Indels: 5
0.69 0.22 0.10
Matches are distributed among these distances:
21 15 0.43
22 5 0.14
23 12 0.34
24 3 0.09
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (21 bp):
TGAATTATATGAAAAGTGATA
Found at i:1606559 original size:40 final size:39
Alignment explanation
Indices: 1606389--1606615 Score: 147
Period size: 40 Copynumber: 5.6 Consensus size: 39
1606379 CTATTAAGGT
* * **
1606389 GTTTGTTTTAAAAATGCCACTAAAGA-ACATTTCTTTTGCGAT
1 GTTTG-TTTAAAAATACCACTAAA-ATATA-TTC-TTTGCGGC
* * * *
1606431 GTTTGTTTATAAACACCACTATAGTACTATGT-TTTAGCGGC
1 GTTTGTTTAAAAATACCACTAAAATA-TAT-TCTTT-GCGGC
* * * * * *
1606472 ATTTGTCTAAAAACACCAC-AATATATGTACTCTATTGCGAC
1 GTTTGTTTAAAAATACCACTAA-A-ATATATTCT-TTGCGGC
*
1606513 GTTTGTTTAAAAATGCCACTAACAAT-TATTCTTATGCGGC
1 GTTTGTTTAAAAATACCACTAA-AATATATTCTT-TGCGGC
* * *
1606553 GTTTGTTTAAAAATATCACTAAAGTATATTCTTTGGCAGC
1 GTTTGTTTAAAAATACCACTAAAATATATTCTTT-GCGGC
1606593 GTTTGTTTAAAAATACCACTAAA
1 GTTTGTTTAAAAATACCACTAAA
1606616 GTACTTATAT
Statistics
Matches: 145, Mismatches: 28, Indels: 26
0.73 0.14 0.13
Matches are distributed among these distances:
39 4 0.03
40 68 0.47
41 60 0.41
42 13 0.09
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (39 bp):
GTTTGTTTAAAAATACCACTAAAATATATTCTTTGCGGC
Found at i:1608315 original size:25 final size:26
Alignment explanation
Indices: 1608281--1608339 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
1608271 TTTTGAAAAC
* *
1608281 ATTTTGAAAATATATATTAT-TA-TAT
1 ATTTTTAAAAAATAT-TTATGTATTAT
1608306 ATTTTTAAAAAATATTTATGTATTAT
1 ATTTTTAAAAAATATTTATGTATTAT
1608332 ATTATTTA
1 ATT-TTTA
1608340 TTCTATTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.14
25 15 0.52
26 6 0.21
27 4 0.14
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.54
Consensus pattern (26 bp):
ATTTTTAAAAAATATTTATGTATTAT
Found at i:1608339 original size:27 final size:27
Alignment explanation
Indices: 1608287--1608339 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
1608277 AAACATTTTG
*
1608287 AAAATATATATTATTATATATTTTTAA
1 AAAATATATATTATTATATATATTTAA
*
1608314 AAAATATTTATGTATTATAT-TATTTA
1 AAAATATATAT-TATTATATATATTTA
1608340 TTCTATTATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 15 0.65
28 8 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
AAAATATATATTATTATATATATTTAA
Found at i:1608364 original size:13 final size:15
Alignment explanation
Indices: 1608336--1608376 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1608326 TATTATATTA
*
1608336 TTTATTCTATTATCA-
1 TTTATT-TATTTTCAT
1608351 TTTA-TTATTTTCAT
1 TTTATTTATTTTCAT
1608365 TTTATTTATTTT
1 TTTATTTATTTT
1608377 TTTGTCCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 7 0.30
14 5 0.22
15 11 0.48
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTATTTTCAT
Found at i:1608520 original size:25 final size:25
Alignment explanation
Indices: 1608460--1608509 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1608450 TGGCAGGCCT
1608460 GACCCAGCAAACCAACCCGGCCAAG
1 GACCCAGCAAACCAACCCGGCCAAG
1608485 GACCCAGCAAACCAACCCGGCCAAG
1 GACCCAGCAAACCAACCCGGCCAAG
1608510 ATTCCAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.44, G:0.20, T:0.00
Consensus pattern (25 bp):
GACCCAGCAAACCAACCCGGCCAAG
Found at i:1609660 original size:8 final size:8
Alignment explanation
Indices: 1609647--1609678 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
1609637 ATTGTTCATT
1609647 TTTTTTTA
1 TTTTTTTA
1609655 TTTTTTTA
1 TTTTTTTA
1609663 TTTCTTTTA
1 TTT-TTTTA
1609672 TTTTTTT
1 TTTTTTT
1609679 CTTAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 15 0.65
9 8 0.35
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTTTTA
Found at i:1609660 original size:9 final size:9
Alignment explanation
Indices: 1609646--1609678 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
1609636 AATTGTTCAT
1609646 TTTTTTTTA
1 TTTTTTTTA
1609655 -TTTTTTTA
1 TTTTTTTTA
*
1609663 TTTCTTTTA
1 TTTTTTTTA
1609672 TTTTTTT
1 TTTTTTT
1609679 CTTAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.09, C:0.03, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1609687 original size:17 final size:17
Alignment explanation
Indices: 1609650--1609688 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1609640 GTTCATTTTT
**
1609650 TTTTATTTTTTTATTTC
1 TTTTATTTTTTTATTAA
*
1609667 TTTTATTTTTTTCTTAA
1 TTTTATTTTTTTATTAA
1609684 TTTTA
1 TTTTA
1609689 GTAATATTTG
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:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTTTATTAA
Found at i:1616680 original size:30 final size:33
Alignment explanation
Indices: 1616632--1616692 Score: 83
Period size: 30 Copynumber: 1.9 Consensus size: 33
1616622 TCTTTTGAAC
1616632 TCAATTTTCTTTTATTCAGTACTTT-TTTTAAT
1 TCAATTTTCTTTTATTCAGTACTTTGTTTTAAT
* *
1616664 TCAA-TTT-TTTTGTTCAGTATTTTGTTTTA
1 TCAATTTTCTTTTATTCAGTACTTTGTTTTA
1616693 TCCTCTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 14 0.54
31 8 0.31
32 4 0.15
ACGTcount: A:0.20, C:0.10, G:0.07, T:0.64
Consensus pattern (33 bp):
TCAATTTTCTTTTATTCAGTACTTTGTTTTAAT
Found at i:1616685 original size:15 final size:15
Alignment explanation
Indices: 1616641--1616686 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1616631 CTCAATTTTC
1616641 TTTTATTCAGTACTTT
1 TTTTATTCAGTA-TTT
1616657 TTTTAATTCA--ATTT
1 TTTT-ATTCAGTATTT
*
1616671 TTTTGTTCAGTATTT
1 TTTTATTCAGTATTT
1616686 T
1 T
1616687 GTTTTATCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 6 0.23
16 4 0.15
17 5 0.19
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.65
Consensus pattern (15 bp):
TTTTATTCAGTATTT
Found at i:1620296 original size:44 final size:44
Alignment explanation
Indices: 1620214--1620298 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
1620204 AATATTTCGC
** * *
1620214 TTAGGGTGAAAACCCAAAAGGGTTCCCTAAGTTTAAAAAAATGT
1 TTAGGGTGAAAACCCAAAAGGGCGCCCTAAATTGAAAAAAATGT
* *
1620258 TTAGGGTGAAAACCCAAATGGGCGCCTTAAATTGAAAAAAA
1 TTAGGGTGAAAACCCAAAAGGGCGCCCTAAATTGAAAAAAA
1620299 AAAGTGGGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.42, C:0.14, G:0.21, T:0.22
Consensus pattern (44 bp):
TTAGGGTGAAAACCCAAAAGGGCGCCCTAAATTGAAAAAAATGT
Found at i:1621852 original size:13 final size:13
Alignment explanation
Indices: 1621834--1621858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1621824 GTTATTTAAT
1621834 ATATATAATATAC
1 ATATATAATATAC
1621847 ATATATAATATA
1 ATATATAATATA
1621859 TAATTTTTGA
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATAATATAC
Found at i:1621906 original size:24 final size:26
Alignment explanation
Indices: 1621874--1621923 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
1621864 TTTGAAAACA
*
1621874 TTTTGAAAATATATAT-TA-TATATT
1 TTTTAAAAATATATATGTATTATATT
*
1621898 TTTTAAAAATATTTATGTATTATATT
1 TTTTAAAAATATATATGTATTATATT
1621924 ATTATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 14 0.64
25 2 0.09
26 6 0.27
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (26 bp):
TTTTAAAAATATATATGTATTATATT
Found at i:1621918 original size:21 final size:23
Alignment explanation
Indices: 1621874--1621918 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
1621864 TTTGAAAACA
1621874 TTTTGAAAATATATATTATATAT
1 TTTTGAAAATATATATTATATAT
* *
1621897 TTTTTAAAA-ATAT-TTATGTAT
1 TTTTGAAAATATATATTATATAT
1621918 T
1 T
1621919 ATATTATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTGAAAATATATATTATATAT
Found at i:1621951 original size:23 final size:24
Alignment explanation
Indices: 1621907--1621967 Score: 74
Period size: 23 Copynumber: 2.6 Consensus size: 24
1621897 TTTTTAAAAA
* *
1621907 TATTTA-TGTATTATATTATTATT
1 TATTTATTTTATTTTATTATTATT
1621930 TA-TTATTTTCATTTTATT-TTATT
1 TATTTATTTT-ATTTTATTATTATT
1621953 TATTTATTTTATTTT
1 TATTTATTTTATTTT
1621968 GGCCTAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 3 0.09
23 16 0.48
24 14 0.42
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (24 bp):
TATTTATTTTATTTTATTATTATT
Found at i:1622097 original size:25 final size:25
Alignment explanation
Indices: 1622048--1622117 Score: 79
Period size: 25 Copynumber: 2.8 Consensus size: 25
1622038 TGGCAGGCCT
**
1622048 GACCCAACAAACCAACCCGGTCAAG
1 GACCCAACAAACCAACCCGACCAAG
*
1622073 GACCCATCAAACCAACCCGACCAA-
1 GACCCAACAAACCAACCCGACCAAG
* *
1622097 GATTCCAACAAACCGACCCGA
1 GA-CCCAACAAACCAACCCGA
1622118 TCCGACCCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
24 2 0.05
25 36 0.95
ACGTcount: A:0.40, C:0.41, G:0.13, T:0.06
Consensus pattern (25 bp):
GACCCAACAAACCAACCCGACCAAG
Found at i:1640065 original size:20 final size:20
Alignment explanation
Indices: 1640026--1640065 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1640016 ATTTCTCGAA
* *
1640026 AGCACATTTTAGGTTGAGGT
1 AGCACATTTTAGGCTAAGGT
1640046 AGCACATTTTAGGCTAAGGT
1 AGCACATTTTAGGCTAAGGT
1640066 GTTATTATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.12, G:0.28, T:0.33
Consensus pattern (20 bp):
AGCACATTTTAGGCTAAGGT
Found at i:1641977 original size:21 final size:21
Alignment explanation
Indices: 1641919--1641980 Score: 115
Period size: 21 Copynumber: 3.0 Consensus size: 21
1641909 GTCATCTCCG
*
1641919 CAGGGTTACATTCCTAACCCT
1 CAGGGTTACATTCCTAGCCCT
1641940 CAGGGTTACATTCCTAGCCCT
1 CAGGGTTACATTCCTAGCCCT
1641961 CAGGGTTACATTCCTAGCCC
1 CAGGGTTACATTCCTAGCCC
1641981 GATAGGTTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.21, C:0.34, G:0.18, T:0.27
Consensus pattern (21 bp):
CAGGGTTACATTCCTAGCCCT
Found at i:1641988 original size:21 final size:22
Alignment explanation
Indices: 1641919--1642030 Score: 112
Period size: 21 Copynumber: 5.3 Consensus size: 22
1641909 GTCATCTCCG
*
1641919 CAGGGTTACATTCCTAACCC-T
1 CAGGGTTACATTCCTAGCCCGT
1641940 CAGGGTTACATTCCTAGCCC-T
1 CAGGGTTACATTCCTAGCCCGT
1641961 CAGGGTTACATTCCTAGCCCGAT
1 CAGGGTTACATTCCTAGCCCG-T
* *
1641984 -A-GGTTATATGCCTAGCCCGAT
1 CAGGGTTACATTCCTAGCCCG-T
* *
1642005 -A-GGTTATATGCCTAGCCCG-
1 CAGGGTTACATTCCTAGCCCGT
1642024 CAGGGTT
1 CAGGGTT
1642031 TTATGACACC
Statistics
Matches: 84, Mismatches: 3, Indels: 8
0.88 0.03 0.08
Matches are distributed among these distances:
20 1 0.01
21 81 0.96
22 1 0.01
23 1 0.01
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (22 bp):
CAGGGTTACATTCCTAGCCCGT
Found at i:1642705 original size:14 final size:14
Alignment explanation
Indices: 1642680--1642716 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1642670 GTATGATTTT
1642680 ATTGATAACATATAC
1 ATTGA-AACATATAC
1642695 ATTGAAACATATAC
1 ATTGAAACATATAC
*
1642709 ATTAAAAC
1 ATTGAAAC
1642717 CAACTTATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 16 0.76
15 5 0.24
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (14 bp):
ATTGAAACATATAC
Found at i:1642874 original size:31 final size:31
Alignment explanation
Indices: 1642838--1642938 Score: 82
Period size: 31 Copynumber: 3.2 Consensus size: 31
1642828 TTATCCAATA
1642838 TATTCAAACAACCAACTGATCACTTCACATT
1 TATTCAAACAACCAACTGATCACTTCACATT
** * * * * *
1642869 TATTCAATTTATCC-A-T-AACATTTTATCCAATA
1 TATTCAA-ACAACCAACTGATCACTTCA--C-ATT
1642901 TATTCAAACAACCAACTGATCACTTCACATT
1 TATTCAAACAACCAACTGATCACTTCACATT
1642932 TATTCAA
1 TATTCAA
1642939 TTTATCCATA
Statistics
Matches: 49, Mismatches: 14, Indels: 14
0.64 0.18 0.18
Matches are distributed among these distances:
29 6 0.12
30 1 0.02
31 21 0.43
32 14 0.29
33 1 0.02
34 6 0.12
ACGTcount: A:0.39, C:0.25, G:0.02, T:0.35
Consensus pattern (31 bp):
TATTCAAACAACCAACTGATCACTTCACATT
Found at i:1642881 original size:63 final size:63
Alignment explanation
Indices: 1642782--1642974 Score: 332
Period size: 63 Copynumber: 3.0 Consensus size: 63
1642772 TTTCATGCTC
* * * *
1642782 ACAACTAACTTATCATTTCACATTTATTCAGTTTATCCATAACATTTTATCCAATATATTCAA
1 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
1642845 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
1 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
*
1642908 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCATA
1 ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCA-A
1642972 ACA
1 ACA
1642975 TTTTATCCAA
Statistics
Matches: 124, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
63 120 0.97
64 4 0.03
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.38
Consensus pattern (63 bp):
ACAACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATATATTCAA
Found at i:1642899 original size:23 final size:23
Alignment explanation
Indices: 1642867--1642989 Score: 107
Period size: 23 Copynumber: 5.6 Consensus size: 23
1642857 TCACTTCACA
*
1642867 TTTATTCAATTTATCCATAACAT
1 TTTATCCAATTTATCCATAACAT
* *
1642890 TTTATCCAATATATTCA-AACA-
1 TTTATCCAATTTATCCATAACAT
* * * *
1642911 ---A-CCAACTGATCACTTCACA-
1 TTTATCCAATTTATC-CATAACAT
*
1642930 TTTATTCAATTTATCCATAACAT
1 TTTATCCAATTTATCCATAACAT
*
1642953 TTTATCCAATTTATTCATAACAT
1 TTTATCCAATTTATCCATAACAT
1642976 TTTATCCAATTTAT
1 TTTATCCAATTTAT
1642990 TCAAACTTCA
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
17 6 0.08
18 2 0.03
19 3 0.04
22 10 0.13
23 56 0.73
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.43
Consensus pattern (23 bp):
TTTATCCAATTTATCCATAACAT
Found at i:1642990 original size:23 final size:23
Alignment explanation
Indices: 1642930--1642992 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
1642920 TCACTTCACA
* *
1642930 TTTATTCAATTTATCCATAACAT
1 TTTATCCAATTTATTCATAACAT
1642953 TTTATCCAATTTATTCATAACAT
1 TTTATCCAATTTATTCATAACAT
1642976 TTTATCCAATTTATTCA
1 TTTATCCAATTTATTCA
1642993 AACTTCACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.33, C:0.17, G:0.00, T:0.49
Consensus pattern (23 bp):
TTTATCCAATTTATTCATAACAT
Found at i:1643820 original size:26 final size:25
Alignment explanation
Indices: 1643768--1643866 Score: 62
Period size: 26 Copynumber: 3.9 Consensus size: 25
1643758 TTGATTAATA
* *
1643768 TTATATAA-ATTATTTATATTGTAATT
1 TTATAAAATATTAATTATATT-T-ATT
1643794 TTATAAAATGATTAATTATATTTATT
1 TTATAAAAT-ATTAATTATATTTATT
* *
1643820 TAATATAATAGTTAA-TATTATTTATT
1 TTATAAAATA-TTAATTA-TATTTATT
* *
1643846 ATAAAAAATTATT-ATTA-ATTT
1 TTATAAAA-TATTAATTATATTT
1643867 TAAAATATTA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
24 4 0.07
25 4 0.07
26 37 0.63
27 3 0.05
28 11 0.19
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (25 bp):
TTATAAAATATTAATTATATTTATT
Found at i:1643860 original size:20 final size:20
Alignment explanation
Indices: 1643835--1643876 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1643825 TAATAGTTAA
*
1643835 TATTATTTATTATAAAAAAT
1 TATTATTAATTATAAAAAAT
* *
1643855 TATTATTAATTTTAAAATAT
1 TATTATTAATTATAAAAAAT
1643875 TA
1 TA
1643877 AAATAATTCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TATTATTAATTATAAAAAAT
Found at i:1646889 original size:38 final size:39
Alignment explanation
Indices: 1646823--1646930 Score: 103
Period size: 38 Copynumber: 2.7 Consensus size: 39
1646813 CTTACTTAGC
* * *
1646823 AAATCCTTCGAGCCATC-AGTAAGTCTTTCAAGC-ATGAT
1 AAATCCTTAGGGCCATCTA-TAAGCCTTTCAAGCAATGAT
* *
1646861 AAATCCTTAGGGTCATCTATAAGCCTTTCGAGCAAGATGAT
1 AAATCCTTAGGGCCATCTATAAGCCTTTCAAGC-A-ATGAT
* *
1646902 AAGTCCTTCGGGCCATCTATAAGACCTTT
1 AAATCCTTAGGGCCATCTATAAG-CCTTT
1646931 GGGCATGATG
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
38 26 0.46
39 1 0.02
41 25 0.44
42 5 0.09
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (39 bp):
AAATCCTTAGGGCCATCTATAAGCCTTTCAAGCAATGAT
Found at i:1646909 original size:41 final size:43
Alignment explanation
Indices: 1646851--1646930 Score: 119
Period size: 41 Copynumber: 1.9 Consensus size: 43
1646841 GTAAGTCTTT
*
1646851 CAAGCATGATAAATCCTTAGGGTCATCTATAAG-CCTTTCGAG
1 CAAGCATGATAAATCCTTAGGGCCATCTATAAGACCTTTCGAG
* *
1646893 CAAG-ATGATAAGTCCTTCGGGCCATCTATAAGACCTTT
1 CAAGCATGATAAATCCTTAGGGCCATCTATAAGACCTTT
1646931 GGGCATGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
41 25 0.74
42 9 0.26
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (43 bp):
CAAGCATGATAAATCCTTAGGGCCATCTATAAGACCTTTCGAG
Found at i:1647114 original size:236 final size:238
Alignment explanation
Indices: 1646694--1647418 Score: 963
Period size: 236 Copynumber: 3.1 Consensus size: 238
1646684 TAAGTCCTTC
* * **
1646694 GGCAGGATGTTTTCACATGATTTTCAAAAAAATGAGAAAGCGATTTCCAAAAATTCTCATTTAAA
1 GGCATGATGTTTTCACATGATTTTC-GAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAA
* * * ** *
1646759 -CATTTTCTGAAAACTGATTTTTTTAAAAAGGTACGAAAACAATTTACAAAGTTTCTTACTTAGC
65 TC-TTTTCTGAAAATTGATTTTTTT-AAAA-GAAAGAAAATGATTTACAAAGTTTCTTA-TTAGT
* * *
1646823 AAATCCTTC-GAGCCATCAGTAAGTCTTTCAAGC---ATG-ATAAATCCTTAGGGTCATCTATAA
126 AAGTCCTTCGGA-CCATCAATAAGTCTTTCAAGCATGATGCATAAATCCTTTGGGTCATCTATAA
*
1646883 GCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTG
190 GCCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTTG
* * *
1646932 GGCATGATGTTTCCAAATGATTTTCGAAAAATGAGAAAGCGGTTTCCAAAGTTTCTCATTTAAAT
1 GGCATGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAAT
*
1646997 C-TTTCTGAAAATTGATTTTTTTGAAAAG-AAGAAAATGATTTCCAAAGTTTCTT-TTAGTAAGT
66 CTTTTCTGAAAATTGATTTTTTT-AAAAGAAAGAAAATGATTTACAAAGTTTCTTATTAGTAAGT
* * *
1647059 CCTTCGGACCATCATTAAGTCTTTTAAGCATGATGCATAAATCTTTTGGGTCATCTATAAGCCTT
130 CCTTCGGACCATCAATAAGTCTTTCAAGCATGATGCATAAATCCTTTGGGTCATCTATAAGCCTT
* *
1647124 TCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAAACCTTGG
195 TCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTTG
* *
1647168 GGCAAGATGTTTTCACATGATTTT-G-AAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAAAT
1 GGCATGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAAT
* *
1647231 CTTTTTTGAAAATTGA--TTTTTAAAAGAAAGAAAATGATTTTCAAAGTTTCTTACTTAGTAAGT
66 CTTTTCTGAAAATTGATTTTTTTAAAAGAAAGAAAATGATTTACAAAGTTTCTTA-TTAGTAAGT
* * *
1647294 CCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCATAAATCCTTTAGGTCATCTATAAGCCTT
130 CCTTCGGACCATCAATAAGTCTTTCAAGCATGATGCATAAATCCTTTGGGTCATCTATAAGCCTT
* * * *
1647359 TCGAGCAAGATGATAAGTCATCCGGACCATCTGTAAGACTTTTTG
195 TCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGAC-CTTTG
*
1647404 GGCATGACGTTTTCA
1 GGCATGATGTTTTCA
1647419 TATGGTGTTA
Statistics
Matches: 433, Mismatches: 43, Indels: 24
0.87 0.09 0.05
Matches are distributed among these distances:
232 36 0.08
233 31 0.07
234 58 0.13
235 121 0.28
236 129 0.30
237 35 0.08
238 23 0.05
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (238 bp):
GGCATGATGTTTTCACATGATTTTCGAAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAAT
CTTTTCTGAAAATTGATTTTTTTAAAAGAAAGAAAATGATTTACAAAGTTTCTTATTAGTAAGTC
CTTCGGACCATCAATAAGTCTTTCAAGCATGATGCATAAATCCTTTGGGTCATCTATAAGCCTTT
CGAGCAAGATGATAAGTCATTCGGGCCATCTATAAGACCTTTG
Found at i:1647352 original size:235 final size:237
Alignment explanation
Indices: 1646694--1647390 Score: 923
Period size: 235 Copynumber: 2.9 Consensus size: 237
1646684 TAAGTCCTTC
* * **
1646694 GGCAGGATGTTTTCACATGATTTTCAAAAAAATGAGAAAGCGATTTCCAAAAATTCTCATTTAAA
1 GGCAAGATGTTTTCACATGATTTT--AGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAA
* * ** *
1646759 -CATTTTCTGAAAACTGATTTTTTTAAAAAGGTACGAAAACAATTTACAAAGTTTCTTACTTAGC
64 TC-TTTTCTGAAAATTGA-TTTTTTAAAAA-G-AAGAAAATGATTTACAAAGTTTCTTACTTAGT
* * *
1646823 AAATCCTTCGAGCCATCAGTAAGTCTTTCAAGC---ATG-ATAAATCC-TTAGGGTCATCTATAA
125 AAGTCCTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCATAAATCCTTTA-GGTCATCTATAA
* * *
1646883 GCCTTTCGAGCAAGATGATAAGTCCTTCGGGCCATCTATAAGACCTTTG
189 GCCTTTCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAAACCTTGG
* * * * *
1646932 GGCATGATGTTTCCAAATGATTTTCGAAAAATGAGAAAGCGGTTTCCAAAGTTTCTCATTTAAAT
1 GGCAAGATGTTTTCACATGATTTTAG-AAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAAT
* *
1646997 C-TTTCTGAAAATTGATTTTTTTGAAAAGAAGAAAATGATTTCCAAAGTTTCTT--TTAGTAAGT
65 CTTTTCTGAAAATTGA-TTTTTTAAAAAGAAGAAAATGATTTACAAAGTTTCTTACTTAGTAAGT
* * * * *
1647059 CCTTCGGACCATCATTAAGTCTTTTAAGCATGATGCATAAATCTTTTGGGTCATCTATAAGCCTT
129 CCTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCATAAATCCTTTAGGTCATCTATAAGCCTT
1647124 TCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAAACCTTGG
194 TCGAGCAAGATGATAAGTCATTCGGGCCATCTATAAAACCTTGG
*
1647168 GGCAAGATGTTTTCACATGATTTT-GAAAATGAGAAAGCAATTTCCAAAGTTTCTCATTTAAATC
1 GGCAAGATGTTTTCACATGATTTTAGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATC
* *
1647232 TTTTTTGAAAATTGA-TTTTT-AAAAGAAAGAAAATGATTTTCAAAGTTTCTTACTTAGTAAGTC
66 TTTTCTGAAAATTGATTTTTTAAAAAG-AAGAAAATGATTTACAAAGTTTCTTACTTAGTAAGTC
*
1647295 CTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCATAAATCCTTTAGGTCATCTATAAGCCTTT
130 CTTCGGGCCATCAATAAGTCTTTCAAGCATGATGCATAAATCCTTTAGGTCATCTATAAGCCTTT
* *
1647360 CGAGCAAGATGATAAGTCATCCGGACCATCT
195 CGAGCAAGATGATAAGTCATTCGGGCCATCT
1647391 GTAAGACTTT
Statistics
Matches: 408, Mismatches: 40, Indels: 25
0.86 0.08 0.05
Matches are distributed among these distances:
232 37 0.09
233 29 0.07
234 58 0.14
235 116 0.28
236 110 0.27
237 36 0.09
238 22 0.05
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (237 bp):
GGCAAGATGTTTTCACATGATTTTAGAAAATGAGAAAGCGATTTCCAAAGTTTCTCATTTAAATC
TTTTCTGAAAATTGATTTTTTAAAAAGAAGAAAATGATTTACAAAGTTTCTTACTTAGTAAGTCC
TTCGGGCCATCAATAAGTCTTTCAAGCATGATGCATAAATCCTTTAGGTCATCTATAAGCCTTTC
GAGCAAGATGATAAGTCATTCGGGCCATCTATAAAACCTTGG
Found at i:1647483 original size:17 final size:15
Alignment explanation
Indices: 1647461--1647503 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
1647451 TAAAAAAGAG
1647461 AAAAATAAAATATGCTA
1 AAAAATAAAAT-TGC-A
*
1647478 AAAAATGAGAATTGCA
1 AAAAAT-AAAATTGCA
1647494 AAAAATAAAA
1 AAAAATAAAA
1647504 GAAGTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.13
16 7 0.30
17 9 0.39
18 4 0.17
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (15 bp):
AAAAATAAAATTGCA
Found at i:1648186 original size:117 final size:117
Alignment explanation
Indices: 1647980--1648210 Score: 354
Period size: 117 Copynumber: 2.0 Consensus size: 117
1647970 CACTTTGTTT
* * *
1647980 GATTCCATCACAGAAGAAGGTGGATCAACATTTCTAGTGAAGAGTTCATAATGAGAAGAACTCAT
1 GATTCCACCACAGAAGAAGATGGATCAACATTTCTAGTGAAGAGTTCATAATGAGAAGAACTCAA
*
1648045 CTAAAGAAGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGTTC
66 CCAAAGAAGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGTTC
* * * *
1648097 GATTCCACCACAGAAGGAGATGGATCGACATTTCTAGTGGAGAGTTCGTAATGAGAAGAACTCAA
1 GATTCCACCACAGAAGAAGATGGATCAACATTTCTAGTGAAGAGTTCATAATGAGAAGAACTCAA
* * * *
1648162 CCGATGAGGGAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTAG
66 CCAAAGAAGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAG
1648211 CTTGATCCTA
Statistics
Matches: 102, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 102 1.00
ACGTcount: A:0.38, C:0.15, G:0.23, T:0.24
Consensus pattern (117 bp):
GATTCCACCACAGAAGAAGATGGATCAACATTTCTAGTGAAGAGTTCATAATGAGAAGAACTCAA
CCAAAGAAGGAGAAAAAGTTCATAATGAGAAGAACTTGTTCAACCTTAGTTC
Found at i:1649149 original size:20 final size:20
Alignment explanation
Indices: 1649121--1649165 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1649111 AATCAAAATG
1649121 TTTAAGAG-TGTTTTGGGGT
1 TTTAAGAGTTGTTTTGGGGT
*
1649140 ATTTAGGAGTTTGTTTTGGGGT
1 -TTTAAGAG-TTGTTTTGGGGT
1649162 TTTA
1 TTTA
1649166 TACCCAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 7 0.32
21 4 0.18
22 11 0.50
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (20 bp):
TTTAAGAGTTGTTTTGGGGT
Found at i:1651396 original size:2 final size:2
Alignment explanation
Indices: 1651391--1651424 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1651381 AATTTTTTTA
1651391 AT AT AT AT AT AT AT AT A- 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 A
1651425 CGTGAAACGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1651411 original size:17 final size:17
Alignment explanation
Indices: 1651389--1651424 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
1651379 ATAATTTTTT
1651389 TAATATATATATATATA
1 TAATATATATATATATA
1651406 TAATATATATATATATA
1 TAATATATATATATATA
1651423 TA
1 TA
1651425 CGTGAAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TAATATATATATATATA
Found at i:1651413 original size:15 final size:15
Alignment explanation
Indices: 1651393--1651422 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1651383 TTTTTTTAAT
1651393 ATATATATATATATA
1 ATATATATATATATA
1651408 ATATATATATATATA
1 ATATATATATATATA
1651423 TACGTGAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
ATATATATATATATA
Found at i:1652753 original size:34 final size:32
Alignment explanation
Indices: 1652705--1652767 Score: 90
Period size: 34 Copynumber: 1.9 Consensus size: 32
1652695 AAAATTATTT
*
1652705 AATTTAATTATTAAAAATATATACTAAAAATAAA
1 AATTAAATTATTAAAAA-A-ATACTAAAAATAAA
*
1652739 AATTAAATTGTTAAAAAAATACTAAAAAT
1 AATTAAATTATTAAAAAAATACTAAAAAT
1652768 GCTATTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 11 0.41
33 1 0.04
34 15 0.56
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.33
Consensus pattern (32 bp):
AATTAAATTATTAAAAAAATACTAAAAATAAA
Found at i:1653765 original size:78 final size:77
Alignment explanation
Indices: 1653668--1653832 Score: 289
Period size: 78 Copynumber: 2.1 Consensus size: 77
1653658 TTAACACTTT
*
1653668 TTTAAGTTT-ATCAAACAATACCTTCATCTCTAATTACTCAAAATATAGATTTATCAAATAATCT
1 TTTAATTTTAATCAAACAATACCTTCATCTCTAATTACTCAAAATATAGATTTATCAAATAATCT
1653732 AATTATAATAAATA
66 AA-T-TAATAAATA
1653746 TTTAATTTTAATC-AACAATACCTTCATCTCTAATTACTCAAAATATAGATTTATCAAATAATCT
1 TTTAATTTTAATCAAACAATACCTTCATCTCTAATTACTCAAAATATAGATTTATCAAATAATCT
1653810 AATTAATAAATA
66 AATTAATAAATA
1653822 TTTAATTTTAA
1 TTTAATTTTAA
1653833 AAAAAAATTA
Statistics
Matches: 85, Mismatches: 1, Indels: 4
0.94 0.01 0.04
Matches are distributed among these distances:
76 20 0.24
77 1 0.01
78 61 0.72
79 3 0.04
ACGTcount: A:0.44, C:0.13, G:0.02, T:0.41
Consensus pattern (77 bp):
TTTAATTTTAATCAAACAATACCTTCATCTCTAATTACTCAAAATATAGATTTATCAAATAATCT
AATTAATAAATA
Found at i:1654836 original size:20 final size:20
Alignment explanation
Indices: 1654813--1654850 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1654803 ATTCGTTGCG
1654813 ATTTTACTATTCACGTTGTA
1 ATTTTACTATTCACGTTGTA
*
1654833 ATTTTACTATTCATGTTG
1 ATTTTACTATTCACGTTG
1654851 CGAAATTGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.53
Consensus pattern (20 bp):
ATTTTACTATTCACGTTGTA
Found at i:1654887 original size:20 final size:20
Alignment explanation
Indices: 1654864--1654979 Score: 114
Period size: 20 Copynumber: 5.8 Consensus size: 20
1654854 AATTGGAGTT
*
1654864 CGCGTTGTGAATTTGACTTC
1 CGCGTTGCGAATTTGACTTC
*
1654884 CGCGTTGCGAATTTGACTTT
1 CGCGTTGCGAATTTGACTTC
* *
1654904 TGTGTTGCGAATTTGACTAT-
1 CGCGTTGCGAATTTGACT-TC
1654924 CGCGTTGCGAATTTGACTTC
1 CGCGTTGCGAATTTGACTTC
* *
1654944 TGTGTTGCG-ATTT-ACAGATT-
1 CGCGTTGCGAATTTGAC---TTC
1654964 CGCGTTGCGAATTTGA
1 CGCGTTGCGAATTTGA
1654980 AAAATCGCAA
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
18 2 0.03
19 5 0.06
20 64 0.81
21 7 0.09
22 1 0.01
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (20 bp):
CGCGTTGCGAATTTGACTTC
Found at i:1654891 original size:40 final size:41
Alignment explanation
Indices: 1654847--1654934 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 41
1654837 TACTATTCAT
*
1654847 GTTGCGAAATTGGA-GTTCGCGTTGTGAATTTGACT-TCCGC
1 GTTGCGAAATTGGACGTTCGCGTTGCGAATTTGACTAT-CGC
* * * *
1654887 GTTGCG-AATTTGACTTTTGTGTTGCGAATTTGACTATCGC
1 GTTGCGAAATTGGACGTTCGCGTTGCGAATTTGACTATCGC
1654927 GTTGCGAA
1 GTTGCGAA
1654935 TTTGACTTCT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
39 6 0.15
40 32 0.80
41 2 0.05
ACGTcount: A:0.18, C:0.16, G:0.28, T:0.38
Consensus pattern (41 bp):
GTTGCGAAATTGGACGTTCGCGTTGCGAATTTGACTATCGC
Found at i:1654935 original size:40 final size:40
Alignment explanation
Indices: 1654867--1654979 Score: 151
Period size: 40 Copynumber: 2.8 Consensus size: 40
1654857 TGGAGTTCGC
* *
1654867 GTTGTGAATTTGACT-TCCGCGTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTAT-CGCGTTGCGAATTTGACTTCTGT
1654907 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
*
1654947 GTTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGA
1 GTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGA
1654980 AAAATCGCAA
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
38 2 0.03
39 5 0.07
40 59 0.88
41 1 0.01
ACGTcount: A:0.18, C:0.16, G:0.26, T:0.41
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
Found at i:1654971 original size:60 final size:60
Alignment explanation
Indices: 1654863--1654979 Score: 148
Period size: 60 Copynumber: 1.9 Consensus size: 60
1654853 AAATTGGAGT
* * * *
1654863 TCGCGTTGTGAATTTGACTTCCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTTCCGCGTTGCGAATTTGACATTCGCGTTGCGAATTTGACTA
* *
1654923 TCGCGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGA
1 TCGCGTTGCGAATTTGACTTCCGCGTTGCGAATTTGAC--ATTCGCGTTGCGAATTTGA
1654980 AAAATCGCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
58 2 0.04
59 4 0.08
60 43 0.88
ACGTcount: A:0.17, C:0.17, G:0.26, T:0.40
Consensus pattern (60 bp):
TCGCGTTGCGAATTTGACTTCCGCGTTGCGAATTTGACATTCGCGTTGCGAATTTGACTA
Found at i:1654987 original size:21 final size:21
Alignment explanation
Indices: 1654963--1655059 Score: 56
Period size: 20 Copynumber: 4.7 Consensus size: 21
1654953 ATTTACAGAT
1654963 TCGCGTTGCGAATTTGAAAAA
1 TCGCGTTGCGAATTTGAAAAA
*** *
1654984 TCGCAACGCGAATTTGGAAAA
1 TCGCGTTGCGAATTTGAAAAA
** * *
1655005 TCGCAATGCG-ATTT-ACATAT
1 TCGCGTTGCGAATTTGA-AAAA
* * **
1655025 TCGCGTTGCGAAATTG-GAGT
1 TCGCGTTGCGAATTTGAAAAA
1655045 TCGCGTTGCGAATTT
1 TCGCGTTGCGAATTT
1655060 ATTGGTCATT
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (21 bp):
TCGCGTTGCGAATTTGAAAAA
Found at i:1655494 original size:2 final size:2
Alignment explanation
Indices: 1655487--1655523 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1655477 TCGGTCTTAT
1655487 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 T
1655524 TTGCTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1661539 original size:19 final size:19
Alignment explanation
Indices: 1661517--1661580 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
1661507 CATAGCAGAG
1661517 ATCAGAGATCAGAACAAAA
1 ATCAGAGATCAGAACAAAA
* * *
1661536 ATCAGAGATCCGAATAAAT
1 ATCAGAGATCAGAACAAAA
* * * *
1661555 ATCAAAGTTTAGAGCAAAA
1 ATCAGAGATCAGAACAAAA
1661574 ATCAGAG
1 ATCAGAG
1661581 GCCAGATTGT
Statistics
Matches: 34, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (19 bp):
ATCAGAGATCAGAACAAAA
Found at i:1668358 original size:17 final size:18
Alignment explanation
Indices: 1668333--1668375 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
1668323 TCTACCTATA
* *
1668333 TATTATTATTAATATTAT
1 TATTATTATAAAGATTAT
1668351 TA-TATTATAAAGATTAT
1 TATTATTATAAAGATTAT
1668368 TATTATTA
1 TATTATTA
1668376 AACCAATAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTATTATAAAGATTAT
Found at i:1668519 original size:24 final size:23
Alignment explanation
Indices: 1668471--1668539 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 23
1668461 CCCAAAAGAC
* * *
1668471 CCAGAGCCCAAACTAAACTCAGA
1 CCAGAGCCCAAACCAAGCCCAGA
*
1668494 CCTAGAGCCCAAACCAAGCCCCGA
1 CC-AGAGCCCAAACCAAGCCCAGA
* *
1668518 CCCGGGACCCAAACCAAGCCCA
1 CCAGAG-CCCAAACCAAGCCCA
1668540 ACCCTAAGCT
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
23 4 0.11
24 33 0.89
ACGTcount: A:0.36, C:0.43, G:0.16, T:0.04
Consensus pattern (23 bp):
CCAGAGCCCAAACCAAGCCCAGA
Found at i:1677878 original size:42 final size:42
Alignment explanation
Indices: 1677804--1677886 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
1677794 CAAGGGTTTC
* *
1677804 ATGATGCTTAAGTCCTTCAGGCCATCAGTAAGTCTTTCGAGT
1 ATGACGCTTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGT
*
1677846 ATGACGCTTAAATCCTTCAGGTCATCTA-TAAGTCTTTCGAG
1 ATGACGCTTAAATCCTTCAGGCCATC-AGTAAGTCTTTCGAG
1677887 CAAGATGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
42 36 0.97
43 1 0.03
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (42 bp):
ATGACGCTTAAATCCTTCAGGCCATCAGTAAGTCTTTCGAGT
Found at i:1678100 original size:41 final size:40
Alignment explanation
Indices: 1678040--1678140 Score: 114
Period size: 41 Copynumber: 2.5 Consensus size: 40
1678030 CTTAGTAAGC
* *
1678040 CCTTCGGGCCATCAGTAAGT-TTTCGAGCATGATGTTTAAAT
1 CCTTCGGGCCATCA-TAAGTCTTTCGAGCAAGATG-ATAAAT
* * *
1678081 CCTTCGGGTCATCTATAAGTCTTTTGAGCAAGATGATAAGT
1 CCTTCGGGCCATC-ATAAGTCTTTCGAGCAAGATGATAAAT
1678122 CCTTCGGGCCATCCATAAG
1 CCTTCGGGCCAT-CATAAG
1678141 ACCATCGGGC
Statistics
Matches: 51, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
41 37 0.73
42 14 0.27
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.32
Consensus pattern (40 bp):
CCTTCGGGCCATCATAAGTCTTTCGAGCAAGATGATAAAT
Done.