Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001836.1 Hibiscus syriacus cultivar Beakdansim tig00003715_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: 2428596
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 12
Found at i:1546706 original size:31 final size:31
Alignment explanation
Indices: 1546669--1546738 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
1546659 AGTGATAAAT
*
1546669 TAATCACTAACGTTATCGATTTATAACAAAA
1 TAATCACTAACATTATCGATTTATAACAAAA
* *
1546700 TGATCACTAACATTATCGATTTGTAACAAAA
1 TAATCACTAACATTATCGATTTATAACAAAA
1546731 TAATCACT
1 TAATCACT
1546739 CTACTTTCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAATCACTAACATTATCGATTTATAACAAAA
Found at i:1557359 original size:183 final size:187
Alignment explanation
Indices: 1557037--1557427 Score: 623
Period size: 183 Copynumber: 2.1 Consensus size: 187
1557027 TTTTCTAATT
* * *
1557037 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATT-AAAAAAACAGTTTACAATTAATTTAAATAATATATA
*
1557101 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
65 ATTATAAAATAAAAATTTTATATAAATATTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
* * * *
1557166 TTGAATCTTAAATTATTAATTGGGTTTTAAAT-AGTTTGGGTTGAGCCTATATG-T-TA
130 TTGAATCTTAAATTATTAATTGGATTTTAAATGA-TTTGGGCTAAGCCCATATGTTATA
*
1557222 TATATAATATATTTAATATTTTTTAATT-AAAAAACAGTTTACAATTAATTTAAATAATATATAA
1 TATATAATATATTTAATATTTTATAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
*
1557286 TTATAAAATATAAATTTTATATAAA-ATTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
66 TTATAAAATAAAAATTTTATATAAATATTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
*
1557350 TGGATCTTAAATTATTAATTGGATTTTAAATGATTTGGGCTAAGCCCATATGTTATA
131 TGAATCTTAAATTATTAATTGGATTTTAAATGATTTGGGCTAAGCCCATATGTTATA
1557407 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
1557428 AAAATTTTAA
Statistics
Matches: 191, Mismatches: 11, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
183 83 0.43
184 61 0.32
185 30 0.16
186 17 0.09
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (187 bp):
TATATAATATATTTAATATTTTATAATTAAAAAAACAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTTATATAAATATTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTAT
TGAATCTTAAATTATTAATTGGATTTTAAATGATTTGGGCTAAGCCCATATGTTATA
Found at i:1558111 original size:16 final size:16
Alignment explanation
Indices: 1558090--1558120 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1558080 CTTTTAAATT
1558090 AATTAATATAAATTAC
1 AATTAATATAAATTAC
*
1558106 AATTAATTTAAATTA
1 AATTAATATAAATTA
1558121 TTATTTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTAATATAAATTAC
Found at i:1560910 original size:77 final size:76
Alignment explanation
Indices: 1560783--1560938 Score: 249
Period size: 77 Copynumber: 2.0 Consensus size: 76
1560773 CTCATCCACT
* * *
1560783 CCTCAATGTCTCTCAGCTTAAGTCTCCACTCCTCTAATTTCACTGTGAAGGATTGCAAATACGTC
1 CCTCAATGTCTCTCAGCTTAAGTCTCCACTCCTCTAATCTCACCGTGAAGGATTGCAAATACATC
1560848 TGTAGCAAAACA
66 TGTAG-AAAACA
* *
1560860 CCTCAATGTCTCTTAGCTTAAGTCTCCATTCCTCTAATCTCACCGTGAAGGATTGCAAATACATC
1 CCTCAATGTCTCTCAGCTTAAGTCTCCACTCCTCTAATCTCACCGTGAAGGATTGCAAATACATC
*
1560925 TGTAGAAAGCA
66 TGTAGAAAACA
1560936 CCT
1 CCT
1560939 GTTCTTCAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
76 8 0.11
77 65 0.89
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (76 bp):
CCTCAATGTCTCTCAGCTTAAGTCTCCACTCCTCTAATCTCACCGTGAAGGATTGCAAATACATC
TGTAGAAAACA
Found at i:1563314 original size:41 final size:41
Alignment explanation
Indices: 1563257--1563345 Score: 178
Period size: 41 Copynumber: 2.2 Consensus size: 41
1563247 GATGGATTCG
1563257 ATTTAGGATATGACGCCGTTAGTATTGACTAAGTGTCACTC
1 ATTTAGGATATGACGCCGTTAGTATTGACTAAGTGTCACTC
1563298 ATTTAGGATATGACGCCGTTAGTATTGACTAAGTGTCACTC
1 ATTTAGGATATGACGCCGTTAGTATTGACTAAGTGTCACTC
1563339 ATTTAGG
1 ATTTAGG
1563346 CTATCCGTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.27, C:0.16, G:0.22, T:0.35
Consensus pattern (41 bp):
ATTTAGGATATGACGCCGTTAGTATTGACTAAGTGTCACTC
Found at i:1568269 original size:15 final size:15
Alignment explanation
Indices: 1568246--1568295 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
1568236 TAATAGTATT
*
1568246 TTTAATATTTTAATA
1 TTTATTATTTTAATA
1568261 TTTATTATTTTATATA
1 TTTATTATTTTA-ATA
* *
1568277 ATTATTTTTTTGAATA
1 TTTATTATTTT-AATA
1568293 TTT
1 TTT
1568296 GAGTTTTCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 11 0.38
16 17 0.59
17 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (15 bp):
TTTATTATTTTAATA
Found at i:1569733 original size:34 final size:34
Alignment explanation
Indices: 1569690--1569756 Score: 134
Period size: 34 Copynumber: 2.0 Consensus size: 34
1569680 CGATTCATTA
1569690 CCGTTAACAATCATTATTGGGATAACATAATGCG
1 CCGTTAACAATCATTATTGGGATAACATAATGCG
1569724 CCGTTAACAATCATTATTGGGATAACATAATGC
1 CCGTTAACAATCATTATTGGGATAACATAATGC
1569757 TAACTTGTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (34 bp):
CCGTTAACAATCATTATTGGGATAACATAATGCG
Found at i:1573123 original size:41 final size:40
Alignment explanation
Indices: 1573050--1573145 Score: 111
Period size: 41 Copynumber: 2.4 Consensus size: 40
1573040 TTTGTTCAAC
* *
1573050 AAATGATCGATCCCTTTTGAATAGAATCGATCCCTCGAGAG
1 AAATGATCGATCCCTTTTGAAAAGAATCGATCCATCG-GAG
* * * *
1573091 AAATGATCGATCCCTTTTTAAAAGGATTGATCCATTGGAG
1 AAATGATCGATCCCTTTTGAAAAGAATCGATCCATCGGAG
*
1573131 ATAAGGATCGATCCC
1 A-AATGATCGATCCC
1573146 CCGAAAGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 4 0.09
41 43 0.91
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (40 bp):
AAATGATCGATCCCTTTTGAAAAGAATCGATCCATCGGAG
Found at i:1582225 original size:2 final size:2
Alignment explanation
Indices: 1582218--1582259 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1582208 GTCGTTAGTG
1582218 AT 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 AT
1582260 GTATGTAACC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1582874 original size:12 final size:11
Alignment explanation
Indices: 1582803--1582865 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
1582793 AAAATTACAT
1582803 TATTAAAAATA
1 TATTAAAAATA
1582814 TATTAAAAATA
1 TATTAAAAATA
* ***
1582825 CATTATTGATA
1 TATTAAAAATA
*
1582836 -ATTATAACAT-
1 TATTA-AAAATA
1582846 T-TTAAAAATA
1 TATTAAAAATA
1582856 TATTAAAAAT
1 TATTAAAAAT
1582866 TCTATTAAAT
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
9 4 0.10
10 8 0.20
11 28 0.70
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:1583139 original size:78 final size:78
Alignment explanation
Indices: 1583010--1583168 Score: 318
Period size: 78 Copynumber: 2.0 Consensus size: 78
1583000 ATTAATATCT
1583010 TAATTAACAAAATTAATGGCATCAAATCATATTTGAGAGAAAATGATCATCCCTACTACTAACAT
1 TAATTAACAAAATTAATGGCATCAAATCATATTTGAGAGAAAATGATCATCCCTACTACTAACAT
1583075 GTACCATATAAAG
66 GTACCATATAAAG
1583088 TAATTAACAAAATTAATGGCATCAAATCATATTTGAGAGAAAATGATCATCCCTACTACTAACAT
1 TAATTAACAAAATTAATGGCATCAAATCATATTTGAGAGAAAATGATCATCCCTACTACTAACAT
1583153 GTACCATATAAAG
66 GTACCATATAAAG
1583166 TAA
1 TAA
1583169 AACAAAGACA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.28
Consensus pattern (78 bp):
TAATTAACAAAATTAATGGCATCAAATCATATTTGAGAGAAAATGATCATCCCTACTACTAACAT
GTACCATATAAAG
Found at i:1583510 original size:14 final size:14
Alignment explanation
Indices: 1583493--1583554 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
1583483 ATAAACATTG
1583493 AACCCTAAATACTA
1 AACCCTAAATACTA
*
1583507 AACCCTACAA-CCTA
1 AACCCTA-AATACTA
* *
1583521 AACCTTAAATATTA
1 AACCCTAAATACTA
*
1583535 AAACCTAAAT-CATA
1 AACCCTAAATAC-TA
1583549 AACCCT
1 AACCCT
1583555 TAATCCGATT
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
13 2 0.05
14 33 0.89
15 2 0.05
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (14 bp):
AACCCTAAATACTA
Found at i:1583524 original size:28 final size:28
Alignment explanation
Indices: 1583493--1583554 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
1583483 ATAAACATTG
* *
1583493 AACCCTAAATACTAAACCCTACAA-CCTA
1 AACCCTAAATACTAAAACCTA-AATCATA
* *
1583521 AACCTTAAATATTAAAACCTAAATCATA
1 AACCCTAAATACTAAAACCTAAATCATA
1583549 AACCCT
1 AACCCT
1583555 TAATCCGATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (28 bp):
AACCCTAAATACTAAAACCTAAATCATA
Found at i:1583542 original size:42 final size:42
Alignment explanation
Indices: 1583427--1583554 Score: 104
Period size: 42 Copynumber: 3.0 Consensus size: 42
1583417 GCAATTAACT
* ** *
1583427 CTAAACTCTAAACCCTAAACATTAAATTA-C-AAATACTAAATC
1 CTAAACCCTAAACTATAAACATTAAA--ACCTAAATACTAAACC
* * *
1583469 CTAAACCCTAGACTATAAACATTGAACCCTAAATACTAAACC
1 CTAAACCCTAAACTATAAACATTAAAACCTAAATACTAAACC
*
1583511 CTACAA-CCTAAACCT-TAAATATTAAAACCTAAAT-CATAAACC
1 CTA-AACCCTAAA-CTATAAACATTAAAACCTAAATAC-TAAACC
1583553 CT
1 CT
1583555 TAATCCGATT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
41 2 0.03
42 64 0.91
43 4 0.06
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.24
Consensus pattern (42 bp):
CTAAACCCTAAACTATAAACATTAAAACCTAAATACTAAACC
Found at i:1584235 original size:15 final size:16
Alignment explanation
Indices: 1584203--1584236 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1584193 GTTTGAAACA
*
1584203 AGTTTTAATATTTTTG
1 AGTTTTAATATGTTTG
1584219 AGTTTTAATA-GTTTG
1 AGTTTTAATATGTTTG
1584234 AGT
1 AGT
1584237 CGAGTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.26, C:0.00, G:0.18, T:0.56
Consensus pattern (16 bp):
AGTTTTAATATGTTTG
Found at i:1584303 original size:26 final size:26
Alignment explanation
Indices: 1584273--1584328 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
1584263 TTTGAGTTTG
1584273 AGTTGAATTTGATTTGTAAA-TTTTTA
1 AGTTGAATTT-ATTTGTAAAGTTTTTA
* *
1584299 AGTTGAGTTTATTTTTAAAGTTTTTA
1 AGTTGAATTTATTTGTAAAGTTTTTA
1584325 AGTT
1 AGTT
1584329 TGAGTTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 8 0.30
26 19 0.70
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.55
Consensus pattern (26 bp):
AGTTGAATTTATTTGTAAAGTTTTTA
Found at i:1584341 original size:26 final size:25
Alignment explanation
Indices: 1584289--1584342 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
1584279 ATTTGATTTG
**
1584289 TAAATTTTTAAGTTGAGTTTATTTT
1 TAAATTTTTAAGTTGAGTTTAAATT
1584314 TAAAGTTTTTAAGTTTGAG-TTAAATT
1 TAAA-TTTTTAAG-TTGAGTTTAAATT
1584340 TAA
1 TAA
1584343 TAATATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 4 0.16
26 16 0.64
27 5 0.20
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.54
Consensus pattern (25 bp):
TAAATTTTTAAGTTGAGTTTAAATT
Found at i:1594848 original size:95 final size:95
Alignment explanation
Indices: 1594640--1594849 Score: 260
Period size: 95 Copynumber: 2.2 Consensus size: 95
1594630 ACAGATCGTT
* * ** *
1594640 TGATATTATATATGATATCGATACTACTTAGAGTAATAATACCAATACTCTGAGTTATGGTACTG
1 TGATATCATATATGATATCAATACTACTTAGAGTAATAATACCAATACTCTGAG-TACAGTACCG
* * * *
1594705 ATACTGTCAAAACATAATGCTAAATTGGTAC
65 ATACTGTCAAAACAGAATACTAAAATGATAC
* * * * **
1594736 CGATACCATATATGATATCAATACTACTTAGAGTAGTAGTACTGATACTGCTGAG-ACAGTACCG
1 TGATATCATATATGATATCAATACTACTTAGAGTAATAATACCAATACT-CTGAGTACAGTACCG
1594800 ATACTGTCAAAACAGAATACTAAAATGATAC
65 ATACTGTCAAAACAGAATACTAAAATGATAC
1594831 TGATATCATATATGATATC
1 TGATATCATATATGATATC
1594850 GATAATATCG
Statistics
Matches: 96, Mismatches: 17, Indels: 3
0.83 0.15 0.03
Matches are distributed among these distances:
95 50 0.52
96 41 0.43
97 5 0.05
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.31
Consensus pattern (95 bp):
TGATATCATATATGATATCAATACTACTTAGAGTAATAATACCAATACTCTGAGTACAGTACCGA
TACTGTCAAAACAGAATACTAAAATGATAC
Found at i:1606080 original size:43 final size:42
Alignment explanation
Indices: 1606013--1606353 Score: 328
Period size: 43 Copynumber: 8.2 Consensus size: 42
1606003 TGAGAACAAA
* * *
1606013 AAACGCCGCAATAGGTCAAGATCTATAGCGGCGTTTTTTGAAC
1 AAACGCCGCAA-AAGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * *
1606056 AAACGTCACAAAAGATCTATATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAAG-TCGAGATCTATAGCGGCGTTTTTGGAAC
* *
1606099 AAACGCCGCAAAAGGTCGATATCTATAACGGCGTTTTTTGGAAC
1 AAACGCCGCAAAA-GTCGAGATCTATAGCGGCG-TTTTTGGAAC
* * * *
1606143 AAACGTCGCAAAATGTTGAGATCTATCGCGGTGTTTTTGGAAC
1 AAACGCCGCAAAA-GTCGAGATCTATAGCGGCGTTTTTGGAAC
*
1606186 AAATGCCGCAAAATGTCGAGATCTATAGCGGCGTTTTTGGAAC
1 AAACGCCGCAAAA-GTCGAGATCTATAGCGGCGTTTTTGGAAC
* *
1606229 AAACGCAGC-AAA----AG-----TAGCGTCGTTTTTGGAAC
1 AAACGCCGCAAAAGTCGAGATCTATAGCGGCGTTTTTGGAAC
* * * *
1606261 AAACGTCGCAAAAAGTC-AGATTTATAGCGTCATTTTTGGAAC
1 AAACGCCGC-AAAAGTCGAGATCTATAGCGGCGTTTTTGGAAC
* *
1606303 AAACGCCGCAAAAGGTC-AGATTTATAGCGGCGTTTTTGGGAC
1 AAACGCCGCAAAA-GTCGAGATCTATAGCGGCGTTTTTGGAAC
1606345 AAACGCCGC
1 AAACGCCGC
1606354 TAATTACCTT
Statistics
Matches: 252, Mismatches: 32, Indels: 29
0.81 0.10 0.09
Matches are distributed among these distances:
32 24 0.10
34 3 0.01
37 4 0.02
41 4 0.02
42 64 0.25
43 116 0.46
44 37 0.15
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (42 bp):
AAACGCCGCAAAAGTCGAGATCTATAGCGGCGTTTTTGGAAC
Found at i:1606182 original size:87 final size:87
Alignment explanation
Indices: 1606013--1606353 Score: 342
Period size: 87 Copynumber: 4.1 Consensus size: 87
1606003 TGAGAACAAA
* * * *
1606013 AAACGCCGCAATAGGTCAAGATCTATAGCGGCGTTTTTT-GAACAAACGTCACAAAAGATCTATA
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTTGGAACAAACGTCGCAAAAGATCTAGA
1606077 TCTATAGCGGCGTTTTTGGAAC
66 TCTATAGCGGCGTTTTTGGAAC
* *
1606099 AAACGCCGCAAAAGGTCGATATCTATAACGGCGTTTTTTGGAACAAACGTCGCAAAATG-T-TGA
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTTGGAACAAACGTCGCAAAA-GATCT-A
* *
1606162 GATCTATCGCGGTGTTTTTGGAAC
64 GATCTATAGCGGCGTTTTTGGAAC
* *
1606186 AAATGCCGCAAAATGTCGAGATCTATAGCGGCG-TTTTTGGAACAAACG-CAGC--AA-A---AG
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTTGGAACAAACGTC-GCAAAAGATCTAG
*
1606243 -----TAGCGTCGTTTTTGGAAC
65 ATCTATAGCGGCGTTTTTGGAAC
* * * * * * *
1606261 AAACGTCGCAAAAAGTC-AGATTTATAGCGTC-ATTTTTGGAACAAACGCCGCAAAAGGTC-AGA
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTTGGAACAAACGTCGCAAAAGATCTAGA
* *
1606323 TTTATAGCGGCGTTTTTGGGAC
66 TCTATAGCGGCGTTTTTGGAAC
1606345 AAACGCCGC
1 AAACGCCGC
1606354 TAATTACCTT
Statistics
Matches: 214, Mismatches: 24, Indels: 36
0.78 0.09 0.13
Matches are distributed among these distances:
74 29 0.14
75 30 0.14
76 2 0.01
79 2 0.01
80 2 0.01
84 26 0.12
85 1 0.00
86 53 0.25
87 68 0.32
88 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (87 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGGCGTTTTTTGGAACAAACGTCGCAAAAGATCTAGA
TCTATAGCGGCGTTTTTGGAAC
Found at i:1606253 original size:32 final size:32
Alignment explanation
Indices: 1606211--1606273 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
1606201 TCGAGATCTA
1606211 TAGCGGCGTTTTTGGAACAAACG-CAGCAAAAG
1 TAGCGGCGTTTTTGGAACAAACGTC-GCAAAAG
*
1606243 TAGCGTCGTTTTTGGAACAAACGTCGCAAAA
1 TAGCGGCGTTTTTGGAACAAACGTCGCAAAA
1606274 AGTCAGATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 28 0.97
33 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (32 bp):
TAGCGGCGTTTTTGGAACAAACGTCGCAAAAG
Found at i:1606302 original size:42 final size:42
Alignment explanation
Indices: 1606243--1606353 Score: 177
Period size: 42 Copynumber: 2.6 Consensus size: 42
1606233 GCAGCAAAAG
*
1606243 TAGCGTCGTTTTTGGAACAAACGTCGCAAAAAGTCAGATTTA
1 TAGCGTCGTTTTTGGAACAAACGCCGCAAAAAGTCAGATTTA
* *
1606285 TAGCGTCATTTTTGGAACAAACGCCGCAAAAGGTCAGATTTA
1 TAGCGTCGTTTTTGGAACAAACGCCGCAAAAAGTCAGATTTA
* *
1606327 TAGCGGCGTTTTTGGGACAAACGCCGC
1 TAGCGTCGTTTTTGGAACAAACGCCGC
1606354 TAATTACCTT
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 63 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (42 bp):
TAGCGTCGTTTTTGGAACAAACGCCGCAAAAAGTCAGATTTA
Found at i:1606306 original size:74 final size:75
Alignment explanation
Indices: 1606175--1606316 Score: 214
Period size: 74 Copynumber: 1.9 Consensus size: 75
1606165 CTATCGCGGT
* * *
1606175 GTTTTTGGAACAAATGCCGCAAAATGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCAGCAA
1 GTTTTTGGAACAAACGCCGCAAAAAGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCAGCAA
1606240 AAGTAGCGTC
66 AAGTAGCGTC
* * * *
1606250 GTTTTTGGAACAAACGTCGCAAAAAGTC-AGATTTATAGCGTCATTTTTGGAACAAACGCCGCAA
1 GTTTTTGGAACAAACGCCGCAAAAAGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCAGCAA
1606314 AAG
66 AAG
1606317 GTCAGATTTA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
74 35 0.58
75 25 0.42
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (75 bp):
GTTTTTGGAACAAACGCCGCAAAAAGTCGAGATCTATAGCGGCATTTTTGGAACAAACGCAGCAA
AAGTAGCGTC
Found at i:1610560 original size:41 final size:41
Alignment explanation
Indices: 1610503--1610865 Score: 238
Period size: 42 Copynumber: 8.8 Consensus size: 41
1610493 TGGCTTTATT
* * *
1610503 TATTTAGCGG-AGTTTATATAAATATGCCACTAATGTACAAG
1 TATTTAGCGGCA-TTTATATAAAAACGCCACTAAAGTACAAG
*
1610544 TATTTAGCGGCATTTATATAAAAACGCCACTAAAGTACCAG
1 TATTTAGCGGCATTTATATAAAAACGCCACTAAAGTACAAG
** * * * *
1610585 TATTTAGCGGTGTTTGTGCTTAAAACGCCACTAAATTACAAG
1 TATTTAGCGGCATTTAT-ATAAAAACGCCACTAAAGTACAAG
* * * ** * *
1610627 TCTTTGGCGGCATTTTTATACTAATGCCACTACAA-TAC-AT
1 TATTTAGCGGCATTTATATAAAAACGCCACTA-AAGTACAAG
* * *
1610667 TATTTAGCGGCGTTTATATAAAAACACCACTAAAGTACCAG
1 TATTTAGCGGCATTTATATAAAAACGCCACTAAAGTACAAG
* * * * * * * *
1610708 TATTTAACGACGTTTGTGCTTAAAACGCCACTAAAATATAA-
1 TATTTAGCGGCATTTAT-ATAAAAACGCCACTAAAGTACAAG
** ** * * *
1610749 TATTTAGTAGTGTTTATATAAAAAAATGCCACTAACGTACGAG
1 TATTTAGCGGCATTTATAT--AAAAACGCCACTAAAGTACAAG
*
1610792 T-TTTAGCGGCATTTATAT-AAAACGGCACTAAAGTACGAA-
1 TATTTAGCGGCATTTATATAAAAACGCCACTAAAGTAC-AAG
* * *
1610831 TATTT-GCCGGCGTTTGTTTAAAAAACGCCACTAAA
1 TATTTAG-CGGCATTTATAT-AAAAACGCCACTAAA
1610866 AATGCCGCTA
Statistics
Matches: 243, Mismatches: 65, Indels: 27
0.73 0.19 0.08
Matches are distributed among these distances:
39 19 0.08
40 42 0.17
41 88 0.36
42 93 0.38
43 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (41 bp):
TATTTAGCGGCATTTATATAAAAACGCCACTAAAGTACAAG
Found at i:1610641 original size:83 final size:82
Alignment explanation
Indices: 1610528--1610864 Score: 199
Period size: 82 Copynumber: 4.1 Consensus size: 82
1610518 ATATAAATAT
1610528 GCCACTAATGTACAAGTATTTAGCGGCATTTATATAAAAACGCCACTA-AAGTACCAGTATTTAG
1 GCCACTAATGTACAAGTATTTAGCGGCATTTATATAAAAACGCCACTACAA-TA-CAGTATTTAG
*
1610592 CGGTGTTTGTGCTTAAAAC
64 CGGCGTTTGTGCTTAAAAC
* * * ** * *
1610611 GCCACTAAAT-TACAAGTCTTTGGCGGCATTTTTATACTAATGCCACTACAATACATTATTTAGC
1 GCCACT-AATGTACAAGTATTTAGCGGCATTTATATAAAAACGCCACTACAATACAGTATTTAGC
* * *
1610675 GGCGTTTAT-ATAAAAAC
65 GGCGTTTGTGCTTAAAAC
* * * * * * * * * * * * *
1610692 ACCACTAAAGTACCAGTATTTAACGACGTTTGTGCTTAAAACGCCACTAAAATATAATATTTAGT
1 GCCACTAATGTACAAGTATTTAGCGGCATTTAT-ATAAAAACGCCACTACAATACAGTATTTAGC
* * * * * *
1610757 AGTGTTTAT-ATAAAAAAAT
65 GGCGTTTGTGCT--TAAAAC
* * * *
1610776 GCCACTAACGTACGAGT-TTTAGCGGCATTTATAT-AAAACGGCACTA-AAGTACGAATATTT-G
1 GCCACTAATGTACAAGTATTTAGCGGCATTTATATAAAAACGCCACTACAA-TAC-AGTATTTAG
1610837 CCGGCGTTTGT--TTAAAAAAC
64 -CGGCGTTTGTGCTT--AAAAC
1610857 GCCACTAA
1 GCCACTAA
1610865 AAATGCCGCT
Statistics
Matches: 195, Mismatches: 48, Indels: 24
0.73 0.18 0.09
Matches are distributed among these distances:
80 4 0.02
81 54 0.28
82 62 0.32
83 51 0.26
84 24 0.12
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (82 bp):
GCCACTAATGTACAAGTATTTAGCGGCATTTATATAAAAACGCCACTACAATACAGTATTTAGCG
GCGTTTGTGCTTAAAAC
Found at i:1610814 original size:123 final size:124
Alignment explanation
Indices: 1610503--1610866 Score: 375
Period size: 123 Copynumber: 3.0 Consensus size: 124
1610493 TGGCTTTATT
* * * *
1610503 TATTTAGCGGAGTTTATAT-AAATATGCCACTAATGTACAAGTATTTAGCGGCATTTATATAAAA
1 TATTTAGCAGCGTTTATATAAAAAATGCCACTAACGTAC-AGTATTTAGCGGCATTTATATAAAA
* * *
1610567 ACGCCACTAAAGTACCAGTATTTAGCGGTGTTTGTGCTTAAAACGCCACTAAATTACAAG
65 ACGCCACTAAAGTACCAGTATTTAACGGCGTTTGTGCTTAAAACGCCACTAAAATACAAG
* * * * * ** * * *
1610627 TCTTTGGCGGCATTTTTAT-ACTAATGCCACT-ACAATACATTATTTAGCGGCGTTTATATAAAA
1 TATTTAGCAGCGTTTATATAAAAAATGCCACTAAC-GTACAGTATTTAGCGGCATTTATATAAAA
* * *
1610690 ACACCACTAAAGTACCAGTATTTAACGACGTTTGTGCTTAAAACGCCACTAAAATATAA-
65 ACGCCACTAAAGTACCAGTATTTAACGGCGTTTGTGCTTAAAACGCCACTAAAATACAAG
* *
1610749 TATTTAGTAGTGTTTATATAAAAAAATGCCACTAACGTACGAGT-TTTAGCGGCATTTATAT-AA
1 TATTTAGCAGCGTTTATAT-AAAAAATGCCACTAACGTAC-AGTATTTAGCGGCATTTATATAAA
* * * **
1610812 AACGGCACTAAAGTACGAATATTTGCCGGCGTTTGT--TTAAAAAACGCCACTAAAA
64 AACGCCACTAAAGTACCAGTATTTAACGGCGTTTGTGCTT--AAAACGCCACTAAAA
1610867 ATGCCGCTAA
Statistics
Matches: 196, Mismatches: 37, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
121 2 0.01
122 12 0.06
123 123 0.63
124 55 0.28
125 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (124 bp):
TATTTAGCAGCGTTTATATAAAAAATGCCACTAACGTACAGTATTTAGCGGCATTTATATAAAAA
CGCCACTAAAGTACCAGTATTTAACGGCGTTTGTGCTTAAAACGCCACTAAAATACAAG
Found at i:1619269 original size:45 final size:46
Alignment explanation
Indices: 1619213--1619299 Score: 115
Period size: 45 Copynumber: 1.9 Consensus size: 46
1619203 GAGTTATTGG
* * * *
1619213 TATGTGAAAAATGT-TATATGTGAATATGTTTTATATGAAAATGCTC
1 TATGTGAAAAATGTGT-TAAGTGAAAATGTTCTATACGAAAATGCTC
1619259 TATGT-AAAAATGTGTTAAGTGAAAATGTTCTATACGAAAAT
1 TATGTGAAAAATGTGTTAAGTGAAAATGTTCTATACGAAAAT
1619300 AACCTATGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
45 30 0.83
46 6 0.17
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (46 bp):
TATGTGAAAAATGTGTTAAGTGAAAATGTTCTATACGAAAATGCTC
Found at i:1619291 original size:30 final size:30
Alignment explanation
Indices: 1619220--1619291 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 30
1619210 TGGTATGTGA
* * * *
1619220 AAAATGTTATATGTGAATATGTTTTATATG
1 AAAATGTTCTATGTAAAAATGTGTTATATG
*
1619250 AAAATGCTCTATGTAAAAATGTGTTA-AGTG
1 AAAATGTTCTATGTAAAAATGTGTTATA-TG
1619280 AAAATGTTCTAT
1 AAAATGTTCTAT
1619292 ACGAAAATAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 1 0.03
30 34 0.97
ACGTcount: A:0.39, C:0.04, G:0.17, T:0.40
Consensus pattern (30 bp):
AAAATGTTCTATGTAAAAATGTGTTATATG
Found at i:1619307 original size:45 final size:46
Alignment explanation
Indices: 1619213--1619311 Score: 114
Period size: 45 Copynumber: 2.2 Consensus size: 46
1619203 GAGTTATTGG
* * * * *
1619213 TATGTGAAAAATGTTATATGTGAATATGTTTTATATGAAAATGCTC
1 TATGTGAAAAATGTTATAAGTGAAAATGTTCTATACGAAAATACTC
1619259 TATGT-AAAAATGTGT-TAAGTGAAAATGTTCTATACGAAAATAAC-C
1 TATGTGAAAAATGT-TATAAGTGAAAATGTTCTATACGAAAAT-ACTC
1619304 TATGTGAA
1 TATGTGAA
1619312 TGTACACTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
45 36 0.80
46 9 0.20
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.36
Consensus pattern (46 bp):
TATGTGAAAAATGTTATAAGTGAAAATGTTCTATACGAAAATACTC
Found at i:1619490 original size:24 final size:25
Alignment explanation
Indices: 1619430--1619503 Score: 87
Period size: 24 Copynumber: 3.0 Consensus size: 25
1619420 GAGTCGAGGG
* *
1619430 TTCTACGCGGTCCTTTGAGATAAAT
1 TTCTACGCGGTCCTTTGGGACAAAT
* *
1619455 TTCTACGTGGTCCTTTGGGACAGA-
1 TTCTACGCGGTCCTTTGGGACAAAT
* *
1619479 TTCTACGCGGTCATTCGGGACAAAT
1 TTCTACGCGGTCCTTTGGGACAAAT
1619504 CTATGTGGCA
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
24 20 0.50
25 20 0.50
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (25 bp):
TTCTACGCGGTCCTTTGGGACAAAT
Found at i:1620672 original size:11 final size:11
Alignment explanation
Indices: 1620656--1620719 Score: 67
Period size: 11 Copynumber: 5.6 Consensus size: 11
1620646 TGGGGCAATG
1620656 TCGAGCTTGAA
1 TCGAGCTTGAA
*
1620667 TCGAGCTCAGAA
1 TCGAGCT-TGAA
1620679 TCGAGCTTGAA
1 TCGAGCTTGAA
*
1620690 GT-GAGCTCAGAA
1 -TCGAGCT-TGAA
*
1620702 TCGAGCTTCAA
1 TCGAGCTTGAA
1620713 TCGAGCT
1 TCGAGCT
1620720 CGAGTCTCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
11 25 0.57
12 19 0.43
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:1620681 original size:12 final size:12
Alignment explanation
Indices: 1620664--1620720 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
1620654 TGTCGAGCTT
1620664 GAATCGAGCTCA
1 GAATCGAGCTCA
*
1620676 GAATCGAGCT-T
1 GAATCGAGCTCA
1620687 GAAGT-GAGCTCA
1 GAA-TCGAGCTCA
1620699 GAATCGAGCTTC-
1 GAATCGAGC-TCA
1620711 -AATCGAGCTC
1 GAATCGAGCTC
1620721 GAGTCTCAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
10 2 0.05
11 17 0.44
12 18 0.46
13 2 0.05
ACGTcount: A:0.30, C:0.23, G:0.26, T:0.21
Consensus pattern (12 bp):
GAATCGAGCTCA
Found at i:1620686 original size:23 final size:23
Alignment explanation
Indices: 1620656--1620720 Score: 105
Period size: 23 Copynumber: 2.8 Consensus size: 23
1620646 TGGGGCAATG
1620656 TCGAGCTTGAATCGAGCTCAGAA
1 TCGAGCTTGAATCGAGCTCAGAA
1620679 TCGAGCTTGAAGT-GAGCTCAGAA
1 TCGAGCTTGAA-TCGAGCTCAGAA
*
1620702 TCGAGCTTCAATCGAGCTC
1 TCGAGCTTGAATCGAGCTC
1620721 GAGTCTCAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
22 1 0.03
23 37 0.95
24 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
TCGAGCTTGAATCGAGCTCAGAA
Found at i:1620958 original size:16 final size:16
Alignment explanation
Indices: 1620939--1620983 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
1620929 CAACGTTTAG
*
1620939 GTTCATTTATGTTCGT
1 GTTCGTTTATGTTCGT
1620955 GTTCGTTTATGTTCGT
1 GTTCGTTTATGTTCGT
1620971 GTTCGTTTATGTT
1 GTTCGTTTATGTT
1620984 TGTTTATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
GTTCGTTTATGTTCGT
Found at i:1625970 original size:2 final size:2
Alignment explanation
Indices: 1625963--1626092 Score: 253
Period size: 2 Copynumber: 65.5 Consensus size: 2
1625953 CACTTATTTA
1625963 AT 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 AT
1626005 AT 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 AT
1626047 AT 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 AT
1626089 -T AT A
1 AT AT A
1626093 AACAAGCATT
Statistics
Matches: 127, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
1 1 0.01
2 126 0.99
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1626995 original size:24 final size:23
Alignment explanation
Indices: 1626944--1627004 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
1626934 TACAATTAAA
*
1626944 TAATCAAATAATAAAAAATTATG
1 TAATAAAATAATAAAAAATTATG
*
1626967 TAATAAAATAATAATAAATTTAT-
1 TAATAAAATAATAA-AAAATTATG
*
1626990 TGAATAAAAAAATAA
1 T-AATAAAATAATAA
1627005 CAATATACCT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
23 14 0.42
24 19 0.58
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (23 bp):
TAATAAAATAATAAAAAATTATG
Found at i:1634026 original size:84 final size:84
Alignment explanation
Indices: 1633885--1634053 Score: 329
Period size: 84 Copynumber: 2.0 Consensus size: 84
1633875 CTAACTAATT
1633885 CAAAGGAAGTTTTACTGAACTTCATTATGCCTTGGAATATGATTTGCAAGAACACCAATTAATCT
1 CAAAGGAAGTTTTACTGAACTTCATTATGCCTTGGAATATGATTTGCAAGAACACCAATTAATCT
1633950 TAATCGACAAAGAAGCTTA
66 TAATCGACAAAGAAGCTTA
*
1633969 CAAAGGCAGTTTTACTGAACTTCATTATGCCTTGGAATATGATTTGCAAGAACACCAATTAATCT
1 CAAAGGAAGTTTTACTGAACTTCATTATGCCTTGGAATATGATTTGCAAGAACACCAATTAATCT
1634034 TAATCGACAAAGAAGCTTA
66 TAATCGACAAAGAAGCTTA
1634053 C
1 C
1634054 TTGGAATATC
Statistics
Matches: 84, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 84 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (84 bp):
CAAAGGAAGTTTTACTGAACTTCATTATGCCTTGGAATATGATTTGCAAGAACACCAATTAATCT
TAATCGACAAAGAAGCTTA
Found at i:1634905 original size:21 final size:21
Alignment explanation
Indices: 1634881--1634928 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1634871 GTGATAATTC
1634881 ACAATACTGACATGGCGTTCT
1 ACAATACTGACATGGCGTTCT
**
1634902 ACAATACTGACATGGTTTTCT
1 ACAATACTGACATGGCGTTCT
1634923 ACAATA
1 ACAATA
1634929 ATGTCGTGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (21 bp):
ACAATACTGACATGGCGTTCT
Found at i:1635971 original size:47 final size:46
Alignment explanation
Indices: 1635875--1635972 Score: 126
Period size: 47 Copynumber: 2.1 Consensus size: 46
1635865 CACGTAGGGG
* * *
1635875 TATAGCGCGGGGCAGGGGCCGCACCTTACCTTTAATTCTGATTTATA
1 TATAGCACGGGGCAGGGGCCGCACCATACCTTTAA-TCTGATTAATA
*
1635922 TATAGCACGGGGCAGGGGTCGCACCATACCTTTAA-CTGATATAACTA
1 TATAGCACGGGGCAGGGGCCGCACCATACCTTTAATCTGAT-TAA-TA
1635969 TATA
1 TATA
1635973 AGGCGCAGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
45 5 0.11
46 2 0.04
47 38 0.84
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (46 bp):
TATAGCACGGGGCAGGGGCCGCACCATACCTTTAATCTGATTAATA
Found at i:1641981 original size:9 final size:9
Alignment explanation
Indices: 1641969--1642002 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
1641959 TAAGTAAAAT
1641969 ATTAAATAA
1 ATTAAATAA
1641978 ATTAAAT-A
1 ATTAAATAA
*
1641986 TTTAAATAA
1 ATTAAATAA
1641995 ATTAAATA
1 ATTAAATA
1642003 CAAAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (9 bp):
ATTAAATAA
Found at i:1641990 original size:17 final size:16
Alignment explanation
Indices: 1641955--1642002 Score: 69
Period size: 17 Copynumber: 2.9 Consensus size: 16
1641945 TGCAAAAAAA
* *
1641955 TAAATAAGTAAAATAT
1 TAAATAAATTAAATAT
1641971 TAAATAAATTAAATATT
1 TAAATAAATTAAATA-T
1641988 TAAATAAATTAAATA
1 TAAATAAATTAAATA
1642003 CAAAATATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (16 bp):
TAAATAAATTAAATAT
Found at i:1643102 original size:23 final size:23
Alignment explanation
Indices: 1643075--1643145 Score: 62
Period size: 23 Copynumber: 3.2 Consensus size: 23
1643065 TCTTTTTTAT
1643075 TTTTAAAAGATTTTGATTCTTTC
1 TTTTAAAAGATTTTGATTCTTTC
** *
1643098 TTTT---ACTTTTCTCATGT-TTT-
1 TTTTAAAAGATTT-TGAT-TCTTTC
1643118 TTTTAAAAGATTTTGATTCTTTC
1 TTTTAAAAGATTTTGATTCTTTC
1643141 TTTTA
1 TTTTA
1643146 CTTTTCTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 14
0.64 0.11 0.25
Matches are distributed among these distances:
20 8 0.23
21 7 0.20
22 7 0.20
23 13 0.37
ACGTcount: A:0.21, C:0.10, G:0.07, T:0.62
Consensus pattern (23 bp):
TTTTAAAAGATTTTGATTCTTTC
Found at i:1643126 original size:43 final size:43
Alignment explanation
Indices: 1643074--1643159 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
1643064 TTCTTTTTTA
1643074 TTTTTAAAAGATTTTGATTCTTTCTTTTACTTTTCTCATGTTT
1 TTTTTAAAAGATTTTGATTCTTTCTTTTACTTTTCTCATGTTT
1643117 TTTTTAAAAGATTTTGATTCTTTCTTTTACTTTTCTCATGTTT
1 TTTTTAAAAGATTTTGATTCTTTCTTTTACTTTTCTCATGTTT
1643160 CAATTTAGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.63
Consensus pattern (43 bp):
TTTTTAAAAGATTTTGATTCTTTCTTTTACTTTTCTCATGTTT
Found at i:1644461 original size:115 final size:115
Alignment explanation
Indices: 1644263--1644520 Score: 265
Period size: 114 Copynumber: 2.2 Consensus size: 115
1644253 TCTAACTTTG
* * *
1644263 AAAAGGAAATAACTTGTTAAATTTATTTTCATGTGAATCTTATATGACTCTGATTGGTAAAAGGA
1 AAAAAGAAATAAATTGTTAAATTTATTTTCATGAGAATCTTATATGACTCTGATTGGTAAAAGGA
* *
1644328 AAAAAAATGTCAAATTTATTTTATTG-GAAATCTAGATTGATTTCATCTTGT
66 AAAAAAATGTCAAATTTA-TTTATTGAG-AATCAAGAATGATTTCATCTTGT
* * * * *
1644379 -AGAAGAAAATAAATTGTTAAATTTACTTTT-AT-AGAATCTTGTATGATTCTGTTTTGTAAAA-
1 AAAAAG-AAATAAATTGTTAAATTTA-TTTTCATGAGAATCTTATATGACTCTGATTGGTAAAAG
** *** * *
1644440 GAAATTAAATCGTTTGATTTATTTCTTGAGAATCAAGAATGATTTTATCTTGT
64 GAAAAAAAAT-GTCAAATTTATTTATTGAGAATCAAGAATGATTTCATCTTGT
* *
1644493 AAAAAGAAATAAATTGTTGACTTTATTT
1 AAAAAGAAATAAATTGTTAAATTTATTT
1644521 CTTAAACGTC
Statistics
Matches: 117, Mismatches: 20, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
113 3 0.03
114 51 0.44
115 39 0.33
116 20 0.17
117 4 0.03
ACGTcount: A:0.38, C:0.07, G:0.14, T:0.41
Consensus pattern (115 bp):
AAAAAGAAATAAATTGTTAAATTTATTTTCATGAGAATCTTATATGACTCTGATTGGTAAAAGGA
AAAAAAATGTCAAATTTATTTATTGAGAATCAAGAATGATTTCATCTTGT
Found at i:1648103 original size:3 final size:3
Alignment explanation
Indices: 1648095--1648119 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1648085 GAATTGGGTT
1648095 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
1648120 ATATCTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1650525 original size:2 final size:2
Alignment explanation
Indices: 1650518--1650559 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1650508 CAAATGATTC
1650518 AT 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 AT
1650560 TGTAATTAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1654261 original size:17 final size:17
Alignment explanation
Indices: 1654239--1654271 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1654229 CTTAAAAAAT
1654239 ATTAATAAACATTTTAA
1 ATTAATAAACATTTTAA
*
1654256 ATTAATAAATATTTTA
1 ATTAATAAACATTTTA
1654272 TGATTAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
ATTAATAAACATTTTAA
Found at i:1655352 original size:23 final size:23
Alignment explanation
Indices: 1655326--1655385 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1655316 ATCAAGCACA
* *
1655326 ATAACATATTAGGTAGCGCTTAT
1 ATAACATAATAGGTAACGCTTAT
*
1655349 ATAACGTAATAGGTAACGCTTAT
1 ATAACATAATAGGTAACGCTTAT
* *
1655372 ATAATAAAATAGGT
1 ATAACATAATAGGT
1655386 TAATTACTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.32
Consensus pattern (23 bp):
ATAACATAATAGGTAACGCTTAT
Found at i:1655372 original size:87 final size:87
Alignment explanation
Indices: 1655221--1655393 Score: 256
Period size: 87 Copynumber: 2.0 Consensus size: 87
1655211 CATTTAACCG
* * * * * * * * *
1655221 GAAATATTATCATGTACAATAGCATATTAGGTACCGTTTATATAATGTAATATGTAGCGTTTATA
1 GAAACATTATCAAGCACAATAACATATTAGGTACCGCTTATATAACGTAATAGGTAACGCTTATA
1655286 TAATAAAATAGGTTAATTACTA
66 TAATAAAATAGGTTAATTACTA
*
1655308 GAAACATTATCAAGCACAATAACATATTAGGTAGCGCTTATATAACGTAATAGGTAACGCTTATA
1 GAAACATTATCAAGCACAATAACATATTAGGTACCGCTTATATAACGTAATAGGTAACGCTTATA
1655373 TAATAAAATAGGTTAATTACT
66 TAATAAAATAGGTTAATTACT
1655394 TAATTTGTTA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (87 bp):
GAAACATTATCAAGCACAATAACATATTAGGTACCGCTTATATAACGTAATAGGTAACGCTTATA
TAATAAAATAGGTTAATTACTA
Found at i:1655936 original size:24 final size:24
Alignment explanation
Indices: 1655909--1655954 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1655899 TTATCAAGGA
1655909 TAACAATAA-AATAATATTATTTAT
1 TAACAA-AATAATAATATTATTTAT
1655933 TAACAAAATAATAATATTATTT
1 TAACAAAATAATAATATTATTT
1655955 TTAGAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.41
Consensus pattern (24 bp):
TAACAAAATAATAATATTATTTAT
Found at i:1656378 original size:200 final size:198
Alignment explanation
Indices: 1655971--1656406 Score: 547
Period size: 200 Copynumber: 2.2 Consensus size: 198
1655961 TAAACATTGC
*
1655971 AAATTTATCTATTACATTATAATTATCGGTTTCGATGTTTTTGAGATCGATACAATTTTAAATGT
1 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGAGATCGATACAATTTTAAATGT
* *
1656036 ATCGACACTTTATGTGTGCACCTCGTTAGACATTCATTCTGGAAAAAAGTATCGACACAAACTCA
66 ACCGACACTTTATGTGTGCACCTCGTTAGACATTCATTATGGAAAAAAGTATCGACACAAACTCA
* * * * *
1656101 AAATGTGTCGATACATTATGTAGACCTATTTTCTCATTAAACTGGTATATTTATACCAAGTACAT
131 AAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACTGATAGATTTATACCAAGTACAT
*
1656166 TGT
196 TAT
* ** * *
1656169 AAATTTACCTATTACATTGTAATTATTAGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAAT
1 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGAGATCGATACAATTT--TAAAT
* * * * ***
1656233 GTACCGACACTTTATGTGTGCATCTCGTTTGGCATTCATTATGGACAAAATGTATCGACAC-TTT
64 GTACCGACACTTTATGTGTGCACCTCGTTAGACATTCATTATGGA-AAAAAGTATCGACACAAAC
* * * *
1656297 TTAAATTTGTGTCGATACATTATGTTGACATATTCTCTCATAAAA-TCGATAGATTTATACC-GG
128 TCAAA-ATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACT-GATAGATTTATACCAAG
*
1656360 TTATATTAT
191 -TACATTAT
*
1656369 AATTTTACCTATTACATTATAATTATCGGTTTCGATGT
1 AAATTTACCTATTACATTATAATTATCGGTTTCGATGT
1656407 AACATATGTG
Statistics
Matches: 202, Mismatches: 30, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
197 3 0.01
198 48 0.24
199 51 0.25
200 100 0.50
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.41
Consensus pattern (198 bp):
AAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTTGAGATCGATACAATTTTAAATGT
ACCGACACTTTATGTGTGCACCTCGTTAGACATTCATTATGGAAAAAAGTATCGACACAAACTCA
AAATGTGTCGATACATTATGTAGACATATTCTCTCATAAAACTGATAGATTTATACCAAGTACAT
TAT
Found at i:1656546 original size:30 final size:31
Alignment explanation
Indices: 1656512--1656596 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 31
1656502 TTATAATAAA
*
1656512 TAAT-AAATATAATTTATAATAA-TTTTATTT
1 TAATAAAATATAA-TAATAATAATTTTTATTT
*
1656542 TAATAAAATATAATAATCATAATTTTTA-TT
1 TAATAAAATATAATAATAATAATTTTTATTT
1656572 T-ATAAAATTATAGAT-ATAAT-ATTTT
1 TAATAAAA-TATA-ATAATAATAATTTT
1656597 AATAGTAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
29 11 0.23
30 22 0.46
31 15 0.31
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (31 bp):
TAATAAAATATAATAATAATAATTTTTATTT
Found at i:1656691 original size:24 final size:24
Alignment explanation
Indices: 1656623--1656691 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 24
1656613 TAAATAATAT
*
1656623 TAAATAAATTATTCTAATATT-TTAA
1 TAAATAAATTA-T-TATTATTGTTAA
1656648 -AAATAAGATTATTATT-TTGTTAA
1 TAAATAA-ATTATTATTATTGTTAA
1656671 TAAATAATATTATT-TTATTGT
1 TAAATAA-ATTATTATTATTGT
1656692 ATTTGATGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
22 2 0.05
23 9 0.24
24 23 0.61
25 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (24 bp):
TAAATAAATTATTATTATTGTTAA
Found at i:1656853 original size:21 final size:21
Alignment explanation
Indices: 1656814--1656854 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1656804 TGGTAAAAAT
* * *
1656814 TACCTAAAATATTATTATTTC
1 TACCTAAAACATCAATATTTC
1656835 TACCTAAAACATCAATATTT
1 TACCTAAAACATCAATATTT
1656855 TTTAACATTT
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:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATCAATATTTC
Found at i:1658051 original size:10 final size:10
Alignment explanation
Indices: 1658027--1658084 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
1658017 TTACATTCTT
*
1658027 TTTTTATTGA
1 TTTTTATTCA
*
1658037 ATTTTATTCA
1 TTTTTATTCA
* *
1658047 CTTTTAATTCT
1 -TTTTTATTCA
1658058 TTTTTATTGCA
1 TTTTTATT-CA
*
1658069 TTTTTATTGA
1 TTTTTATTCA
1658079 TTTTTA
1 TTTTTA
1658085 AAAAAAGTGA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
10 22 0.58
11 16 0.42
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (10 bp):
TTTTTATTCA
Found at i:1658051 original size:21 final size:21
Alignment explanation
Indices: 1658027--1658084 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
1658017 TTACATTCTT
*
1658027 TTTTTATTGAATTTTATT-CA
1 TTTTTATTGATTTTTATTGCA
* **
1658047 CTTTTAATTCTTTTTTATTGCA
1 -TTTTTATTGATTTTTATTGCA
1658069 TTTTTATTGATTTTTA
1 TTTTTATTGATTTTTA
1658085 AAAAAAGTGA
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.21, C:0.07, G:0.05, T:0.67
Consensus pattern (21 bp):
TTTTTATTGATTTTTATTGCA
Found at i:1659640 original size:28 final size:28
Alignment explanation
Indices: 1659602--1659655 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
1659592 TAAAATTTTA
1659602 TATGAAATTC-AGAGGTTAAAATAAAATT
1 TATGAAATTCAAG-GGTTAAAATAAAATT
*
1659630 TATGAAGTTCAAGGGTTAAAATAAAA
1 TATGAAATTCAAGGGTTAAAATAAAA
1659656 ATTTTACCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.50, C:0.04, G:0.17, T:0.30
Consensus pattern (28 bp):
TATGAAATTCAAGGGTTAAAATAAAATT
Found at i:1661203 original size:19 final size:20
Alignment explanation
Indices: 1661179--1661232 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1661169 TGATGCACTA
1661179 GTGCATGGATACACTGCA-G
1 GTGCATGGATACACTGCAGG
* **
1661198 GTGCATGGTTGTACTGCAGG
1 GTGCATGGATACACTGCAGG
1661218 GTGCATGGATACACT
1 GTGCATGGATACACT
1661233 TTGATACCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (20 bp):
GTGCATGGATACACTGCAGG
Found at i:1665452 original size:24 final size:24
Alignment explanation
Indices: 1665425--1665481 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
1665415 ACTATTCTTT
1665425 CGCTTCAATTGAGCTCAAATTTTA
1 CGCTTCAATTGAGCTCAAATTTTA
1665449 CGCTTCAATTGAGCTCAAATTTTA
1 CGCTTCAATTGAGCTCAAATTTTA
*
1665473 GGCTTCAAT
1 CGCTTCAAT
1665482 CGAACTTCTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (24 bp):
CGCTTCAATTGAGCTCAAATTTTA
Found at i:1669106 original size:60 final size:60
Alignment explanation
Indices: 1669008--1669164 Score: 190
Period size: 60 Copynumber: 2.6 Consensus size: 60
1668998 TCTCTAATAA
* * *
1669008 TATGACCTTACCCCTCTCGAGTT-TCAATAAAGGAGGTCAAGCCCTAATCTGCCCTCATCC
1 TATGGCCTTACCCCTCTCGA-TTCTCAATAGAGGAGGTCAAGCCCTAATCTGCCCCCATCC
* * **
1669068 TATGGCCTTACCCCTCTCGATTCTCAATAGAGTAGGTCAGGCTGTAATCTGCCCCCATCC
1 TATGGCCTTACCCCTCTCGATTCTCAATAGAGGAGGTCAAGCCCTAATCTGCCCCCATCC
* * * * *
1669128 TATGGCCTTTCCTCTCTTGGTTCTCTATAGAGGAGGT
1 TATGGCCTTACCCCTCTCGATTCTCAATAGAGGAGGT
1669165 GAGATGAAAT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
59 2 0.02
60 81 0.98
ACGTcount: A:0.20, C:0.31, G:0.18, T:0.31
Consensus pattern (60 bp):
TATGGCCTTACCCCTCTCGATTCTCAATAGAGGAGGTCAAGCCCTAATCTGCCCCCATCC
Found at i:1669329 original size:22 final size:22
Alignment explanation
Indices: 1669290--1669331 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1669280 ACAAAAGGAA
**
1669290 AAAAAGAATATTTCAATTTTCT
1 AAAAAGAATATTAAAATTTTCT
*
1669312 AAAAATAATATTAAAATTTT
1 AAAAAGAATATTAAAATTTT
1669332 ATTTGGTTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
AAAAAGAATATTAAAATTTTCT
Found at i:1670185 original size:16 final size:17
Alignment explanation
Indices: 1670154--1670186 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
1670144 TATATATATA
*
1670154 TATATATATGGATTATT
1 TATATATATAGATTATT
1670171 TATAT-TATAGATTATT
1 TATATATATAGATTATT
1670187 AGATTTTGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TATATATATAGATTATT
Found at i:1670199 original size:7 final size:7
Alignment explanation
Indices: 1670189--1670215 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1670179 AGATTATTAG
1670189 ATTTTGT
1 ATTTTGT
1670196 ATTTTGT
1 ATTTTGT
1670203 ATTTTGT
1 ATTTTGT
1670210 ATTTTG
1 ATTTTG
1670216 AACTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (7 bp):
ATTTTGT
Found at i:1681158 original size:27 final size:28
Alignment explanation
Indices: 1681116--1681180 Score: 109
Period size: 27 Copynumber: 2.4 Consensus size: 28
1681106 TACCCTATCC
1681116 CATT-TAGC-TTCAAAATCATCCCAAAG
1 CATTCTAGCTTTCAAAATCATCCCAAAG
1681142 CATTCTAGCTTTC-AAATCATCCCAAAG
1 CATTCTAGCTTTCAAAATCATCCCAAAG
1681169 CATTCTAGCTTT
1 CATTCTAGCTTT
1681181 TTTCCAATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
26 4 0.11
27 30 0.81
28 3 0.08
ACGTcount: A:0.32, C:0.28, G:0.08, T:0.32
Consensus pattern (28 bp):
CATTCTAGCTTTCAAAATCATCCCAAAG
Found at i:1686065 original size:3 final size:3
Alignment explanation
Indices: 1686057--1686084 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1686047 TGTGTCTTAT
1686057 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1686085 AACCATAAGA
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:1693101 original size:90 final size:90
Alignment explanation
Indices: 1692861--1693588 Score: 1181
Period size: 90 Copynumber: 8.1 Consensus size: 90
1692851 TTTCAAATGC
* * * ** *
1692861 AACTAAACCTTTGGGGGTTTCTTGATTTGTAAGTCCTTCGTGTTATCCATAAGACCTTCAGTGAA
1 AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
*
1692926 TGATGTTTTCAAATGAGATTTTAGA
66 GGATGTTTTCAAATGAGATTTTAGA
*
1692951 AACTAAGCCTTC-AGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
1 AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
*
1693015 GGATGTTTTCAAATAAGATTTTAGA
66 GGATGTTTTCAAATGAGATTTTAGA
*
1693040 AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTACA
1 AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
* * *
1693105 TGATGTTTTCAAATGAGTTTTTTGA
66 GGATGTTTTCAAATGAGATTTTAGA
*
1693130 AACTAAGCCTTCGGGGGTTTTTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
1 AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
1693195 GGATGTTTTCAAATGAGATTTTAGA
66 GGATGTTTTCAAATGAGATTTTAGA
*
1693220 AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGTA
1 AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
* *
1693285 GGGTGTTTTCAAATTAGATTTTAGA
66 GGATGTTTTCAAATGAGATTTTAGA
* * * *
1693310 AACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGTCCTTCGGGCTACCCGTAAGACCTTCAGTGCA
1 AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
*
1693375 GGATATTTTCAAATGAGATTTTAGA
66 GGATGTTTTCAAATGAGATTTTAGA
* *
1693400 AACTAAGCCTTCGGGGGTTTCTTAATATGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
1 AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
*
1693465 AGATGTTTTCAAATGAGATTTTAGA
66 GGATGTTTTCAAATGAGATTTTAGA
* * *
1693490 AACTAAGCCTTC-GGGGTTTCTTGATTTGTAAGTCCTTTGGGTCATCCATAAGACCTTTAGTGCA
1 AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
*
1693554 GGATGTTTTCAAATGAGTTTTTAGA
66 GGATGTTTTCAAATGAGATTTTAGA
1693579 AACTAAGCCT
1 AACTAAGCCT
1693589 GATTTTTAGG
Statistics
Matches: 590, Mismatches: 47, Indels: 3
0.92 0.07 0.00
Matches are distributed among these distances:
89 162 0.27
90 428 0.73
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (90 bp):
AACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCA
GGATGTTTTCAAATGAGATTTTAGA
Found at i:1693702 original size:36 final size:36
Alignment explanation
Indices: 1693632--1693732 Score: 114
Period size: 36 Copynumber: 2.8 Consensus size: 36
1693622 ACAAAAAGTG
*
1693632 AATTTTGTCTCACTTGAGACAATTTTTACTCAAAACA
1 AATTTTGTCTCATTTGAGAC-ATTTTTACTCAAAACA
* * *
1693669 AGTTTTGTCTCTTTTGAGACATTTTT-TTGCAAAACA
1 AATTTTGTCTCATTTGAGACATTTTTACT-CAAAACA
** *
1693705 AATTTCATCTCGTTTGAGACATTTTTAC
1 AATTTTGTCTCATTTGAGACATTTTTAC
1693733 CTGAAACACC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
35 1 0.02
36 35 0.66
37 17 0.32
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.44
Consensus pattern (36 bp):
AATTTTGTCTCATTTGAGACATTTTTACTCAAAACA
Found at i:1693909 original size:36 final size:36
Alignment explanation
Indices: 1693756--1693907 Score: 118
Period size: 36 Copynumber: 4.4 Consensus size: 36
1693746 CTTTGAGATT
* * *
1693756 ATTTCCCTTGAAACGAGTTTTG--TCTCTTGAGACA
1 ATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * *
1693790 GTTTCACTTGAAACAAATTTTGTCTCACTTGAGACA
1 ATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* * ***** *
1693826 GTTTCTTTTGAAACAAA--AAAAATCT-TTGA-ATA
1 ATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
*
1693858 TATTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACA
1 -ATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1693895 ATTTCTCTTGAAA
1 ATTTCTCTTGAAA
1693908 TAGAAAATCT
Statistics
Matches: 88, Mismatches: 23, Indels: 12
0.72 0.19 0.10
Matches are distributed among these distances:
32 2 0.02
33 18 0.20
34 20 0.23
35 3 0.03
36 43 0.49
37 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (36 bp):
ATTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:1693952 original size:67 final size:67
Alignment explanation
Indices: 1693782--1694054 Score: 247
Period size: 67 Copynumber: 4.1 Consensus size: 67
1693772 GTTTTGTCTC
* * * *
1693782 TTGAGA-CAGTTTCACTTGAAAC-AAATTTTGTCTCACTTGAGACAGTTTCTTTTGAAACAAAAA
1 TTGAGATC-GTTTCCCTTGAAACTAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAAC---AA
1693845 AAATCT
62 AAATCT
** * *
1693851 TTGA-ATATATTTCTCTTGAAA-TAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAATAGAAA
1 TTGAGAT-CGTTTCCCTTGAAACTAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACA-AAA
1693914 ATCT
64 ATCT
* * * ***
1693918 TTGAGATCGTTTCCCTTGAAACT-AGTTTTGTCTCTCTTGAGATAGTTT-TCCTTGAAACACCGA
1 TTGAGATCGTTTCCCTTGAAACTAAATTTTGTCTCTCTTGAGACAATTTCT-CTTGAAACAAAAA
1693981 TCT
65 TCT
* * *
1693984 TTGAGATCGTTTCCCTTG-AACTAAATTTTTTCTC-CATGTAGACAATTCCTCTTGAAACACAAA
1 TTGAGATCGTTTCCCTTGAAACTAAATTTTGTCTCTCTTG-AGACAATTTCTCTTGAAACA-AAA
*
1694047 ACCT
64 ATCT
1694051 TTGA
1 TTGA
1694055 TTGTGTTTTC
Statistics
Matches: 166, Mismatches: 27, Indels: 24
0.76 0.12 0.11
Matches are distributed among these distances:
65 7 0.04
66 48 0.29
67 60 0.36
68 4 0.02
69 47 0.28
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (67 bp):
TTGAGATCGTTTCCCTTGAAACTAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAAT
CT
Found at i:1694038 original size:66 final size:65
Alignment explanation
Indices: 1693782--1694046 Score: 207
Period size: 66 Copynumber: 4.0 Consensus size: 65
1693772 GTTTTGTCTC
* * * * *
1693782 TTGAGA-CAGTTTCACTTGAAAC-AAATTTTGTCTCACTTGAGACAGTTTCTTTTGAAACAAAAA
1 TTGAGATC-GTTTCCCTTG-AACTAAATTTTGTCTCTCTTGAGACA-ATTCTCTTGAAAC---AC
1693845 AAATCT
60 AAATCT
** * * * *
1693851 TTGA-ATATATTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAATAGAAAA
1 TTGAGAT-CGTTTCCCTTGAACTAAATTTTGTCTCTCTTGAGACAA-TTCTCTTGAAACA-CAAA
1693915 TCT
63 TCT
* * * * **
1693918 TTGAGATCGTTTCCCTTGAAACT-AGTTTTGTCTCTCTTGAGATAGTTTTCCTTGAAACACCGAT
1 TTGAGATCGTTTCCCTTG-AACTAAATTTTGTCTCTCTTGAGACAATTCT-CTTGAAACACAAAT
1693982 CT
64 CT
* *
1693984 TTGAGATCGTTTCCCTTGAACTAAATTTTTTCTC-CATGTAGACAATTCCTCTTGAAACACAAA
1 TTGAGATCGTTTCCCTTGAACTAAATTTTGTCTCTCTTG-AGACAATT-CTCTTGAAACACAAA
1694047 ACCTTTGATT
Statistics
Matches: 157, Mismatches: 28, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
65 7 0.04
66 52 0.33
67 47 0.30
68 8 0.05
69 43 0.27
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (65 bp):
TTGAGATCGTTTCCCTTGAACTAAATTTTGTCTCTCTTGAGACAATTCTCTTGAAACACAAATCT
Found at i:1694608 original size:91 final size:91
Alignment explanation
Indices: 1694444--1694865 Score: 637
Period size: 91 Copynumber: 4.6 Consensus size: 91
1694434 GATAAACCGA
* * * * *
1694444 TCAACATTGCCAGTAGAGAGTTGATAATGAGAAAAACTCATGCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTACCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
1694509 ATGAGAAGAACTTGTTCAACCTTGGC
66 ATGAGAAGAACTTGTTCAACCTTGAC
** *
1694535 TCGTCATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTACCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
1694600 ATGAGAAGAACTTGTTCAACCTTGGC
66 ATGAGAAGAACTTGTTCAACCTTGAC
* * * * *
1694626 TCAATATTTCCAGTTGAGAGTTCATAATGAGAAGAATTCATCCAACGAGGGAGAAGAAGTTCACA
1 TCAACATTACCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
1694691 ATGAGAAGAACTTGTTCAATCTTGAC
66 ATGAGAAGAACTTGTTCAACCTTGAC
* * *
1694717 TCAACGTTACCAGTGGAGAGTTCGTAATGAGAAGAACTCATCCAACGTGGGAGAAGAAGTTCATA
1 TCAACATTACCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1694782 ATGAGAAGAACTTGTTCAACCTTGAC
66 ATGAGAAGAACTTGTTCAACCTTGAC
* * * *
1694808 TCAACGTTACCAGTTGAGAGTTCATAATGAGAAGAATTCATCCAACGAGGGAAAAGAA
1 TCAACATTACCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAA
1694866 CTGACTCCCG
Statistics
Matches: 302, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
91 302 1.00
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.23
Consensus pattern (91 bp):
TCAACATTACCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGAC
Found at i:1695181 original size:21 final size:22
Alignment explanation
Indices: 1695155--1695200 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
1695145 CGGTAAAAAA
*
1695155 TTACCTAAAACATT-ATTTTTT
1 TTACCTAAAACATTAATGTTTT
1695176 TTACCTAAAACATTAATGTTTT
1 TTACCTAAAACATTAATGTTTT
1695198 TTA
1 TTA
1695201 ACATTTCCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.50
Consensus pattern (22 bp):
TTACCTAAAACATTAATGTTTT
Found at i:1697241 original size:29 final size:28
Alignment explanation
Indices: 1697191--1697269 Score: 70
Period size: 29 Copynumber: 2.8 Consensus size: 28
1697181 TTCTTTGCGT
* *
1697191 TATATTATATTATTTTCCTATTATTATA
1 TATATTATATTATATTACTATTATTATA
* * *
1697219 TATATATATATTATATTATTATTTTTTTA
1 TATAT-TATATTATATTACTATTATTATA
*
1697248 TATATGTTTACTTAT-TTACTAT
1 TATAT-TATA-TTATATTACTAT
1697270 GTTTTTTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
28 5 0.12
29 32 0.78
30 4 0.10
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (28 bp):
TATATTATATTATATTACTATTATTATA
Found at i:1697401 original size:33 final size:35
Alignment explanation
Indices: 1697349--1697429 Score: 98
Period size: 33 Copynumber: 2.4 Consensus size: 35
1697339 CTATGATTAC
*
1697349 TATTTT-TTTAGTTAATATTA-TATGTA-TATTTA-
1 TATTTTATTTATTTAATATTATTAT-TACTATTTAG
*
1697381 TTTTTTATTTATTTAATATTATTATTACTATTTAG
1 TATTTTATTTATTTAATATTATTATTACTATTTAG
1697416 TATTTTATTATATT
1 TATTTTATT-TATT
1697430 ATACATACAT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 5 0.12
33 15 0.37
34 9 0.22
35 8 0.20
36 4 0.10
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.65
Consensus pattern (35 bp):
TATTTTATTTATTTAATATTATTATTACTATTTAG
Found at i:1697414 original size:19 final size:17
Alignment explanation
Indices: 1697360--1697429 Score: 72
Period size: 17 Copynumber: 4.1 Consensus size: 17
1697350 ATTTTTTTAG
*
1697360 TTAATATTATATGTATAT
1 TTAATATTTTAT-TATAT
*
1697378 TT-ATTTTTTATT-TAT
1 TTAATATTTTATTATAT
1697393 TTAATATTATTATTACTAT
1 TTAATATT-TTATTA-TAT
*
1697412 TTAGTATTTTATTATAT
1 TTAATATTTTATTATAT
1697429 T
1 T
1697430 ATACATACAT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
15 5 0.11
16 5 0.11
17 16 0.36
18 8 0.18
19 10 0.23
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.64
Consensus pattern (17 bp):
TTAATATTTTATTATAT
Found at i:1697474 original size:22 final size:22
Alignment explanation
Indices: 1697418--1697508 Score: 82
Period size: 22 Copynumber: 4.2 Consensus size: 22
1697408 CTATTTAGTA
* * *
1697418 TTTTATTATATTATACATACAT
1 TTTTATTATTTTATATATATAT
1697440 TTTTA-TATTTTTATATATATAT
1 TTTTATTA-TTTTATATATATAT
*
1697462 TTTTATTATTTTATTTATACTAT
1 TTTTATTATTTTATATATA-TAT
* *
1697485 TTAT-TTATTTT-CAT-TATAT
1 TTTTATTATTTTATATATATAT
1697504 TTTTA
1 TTTTA
1697509 GTTTCTTTGC
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
19 6 0.11
20 2 0.04
21 3 0.05
22 38 0.67
23 8 0.14
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (22 bp):
TTTTATTATTTTATATATATAT
Found at i:1697476 original size:14 final size:14
Alignment explanation
Indices: 1697442--1697508 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
1697432 ACATACATTT
1697442 TTATATTTTTA-TA
1 TTATATTTTTATTA
1697455 TATATATTTTTATTA
1 T-TATATTTTTATTA
* * *
1697470 TTTTATTTATACTA
1 TTATATTTTTATTA
1697484 TT-TATTTATT-TTCA
1 TTATATTT-TTATT-A
1697498 TTATATTTTTA
1 TTATATTTTTA
1697509 GTTTCTTTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
13 7 0.16
14 28 0.65
15 8 0.19
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATATTTTTATTA
Found at i:1697503 original size:44 final size:43
Alignment explanation
Indices: 1697418--1697507 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
1697408 CTATTTAGTA
*
1697418 TTTTATTATATTATACATACATTTTTATATTTTTATATATATAT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATAT-T
* **
1697462 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATATT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATT
1697505 TTT
1 TTT
1697508 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.10
44 22 0.55
45 12 0.30
46 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (43 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATT
Found at i:1697620 original size:20 final size:19
Alignment explanation
Indices: 1697593--1697648 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1697583 TTTTATCTTC
1697593 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
1697612 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
1697632 A-TTATTTTATATTTATT
1 ATTTATTTTAT-TTTATT
1697649 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:1701948 original size:14 final size:12
Alignment explanation
Indices: 1701931--1701972 Score: 50
Period size: 11 Copynumber: 3.4 Consensus size: 12
1701921 GCAAAAACAA
1701931 AAAAGAAAAGAAGC
1 AAAA-AAAAGAA-C
*
1701945 AAAAAAAACAA-
1 AAAAAAAAGAAC
1701956 AAAAAAAAGAAC
1 AAAAAAAAGAAC
1701968 AAAAA
1 AAAAA
1701973 TCAAAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 10 0.40
12 5 0.20
13 6 0.24
14 4 0.16
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGAAC
Found at i:1701951 original size:25 final size:23
Alignment explanation
Indices: 1701923--1701972 Score: 82
Period size: 25 Copynumber: 2.1 Consensus size: 23
1701913 CAAAAAGGGC
1701923 AAAAACAAAAAAGAAAAGAAGCAAA
1 AAAAACAAAAAA-AAAAGAA-CAAA
1701948 AAAAACAAAAAAAAAAGAACAAA
1 AAAAACAAAAAAAAAAGAACAAA
1701971 AA
1 AA
1701973 TCAAAAAGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 6 0.24
24 7 0.28
25 12 0.48
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (23 bp):
AAAAACAAAAAAAAAAGAACAAA
Found at i:1701957 original size:24 final size:21
Alignment explanation
Indices: 1701923--1701995 Score: 74
Period size: 21 Copynumber: 3.2 Consensus size: 21
1701913 CAAAAAGGGC
1701923 AAAAACAAAAAAGAAAAGAAGCAAA
1 AAAAAC-AAAAAGAAAAGAA-C--A
*
1701948 AAAAACAAAAAAAAAAGAACA
1 AAAAACAAAAAGAAAAGAACA
* *
1701969 AAAATCAAAAAGAAAAGGGACA
1 AAAAACAAAAAGAAAA-GAACA
1701991 AAAAA
1 AAAAA
1701996 ACACATGCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
21 15 0.36
22 8 0.19
23 1 0.02
24 12 0.29
25 6 0.14
ACGTcount: A:0.79, C:0.08, G:0.11, T:0.01
Consensus pattern (21 bp):
AAAAACAAAAAGAAAAGAACA
Found at i:1703708 original size:106 final size:106
Alignment explanation
Indices: 1703581--1704644 Score: 1567
Period size: 106 Copynumber: 10.0 Consensus size: 106
1703571 ATATCGTGCC
* * * * * * * *
1703581 ACTCGAGACAACACAAGTTCAACTTTACAACGAAGGAACCGTTGGTTGTTAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1703646 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1703687 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGATTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1703752 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1703793 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTTAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1703858 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1703899 ACTCCAGACAACGCAAGTTCAACTTCACGACGAATGGACCACTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
1703964 AATTTTAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
1704005 ACTCGAGAGAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTTAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1704070 AATTTCGGAGCCAATTTCAACTTCATAGCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
** *
1704111 ACTCCAGACAACGCAAGTTCAACTTCACGACGAACAGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1704176 AATTTCGGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1704217 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCACTGGTTGTTAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
1704282 AATTTCATAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1704323 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1704388 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
1704429 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1704494 AATTTC-GAAGTCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAG-AGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * *
1704535 ACTCAAGACAACACAAGTTCAACTTCACAATGAAGGGACGGTTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
1704600 GA-TTCTATAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTC-AGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1704641 ACTC
1 ACTC
1704645 GGAACAATGC
Statistics
Matches: 873, Mismatches: 81, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
105 4 0.00
106 869 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1705484 original size:37 final size:37
Alignment explanation
Indices: 1705395--1705498 Score: 127
Period size: 37 Copynumber: 2.8 Consensus size: 37
1705385 CTTTTCGTCA
* * *
1705395 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TACTACGATTCAAACTCCTAAAAATAGGATAGAATTC
* *
1705432 TGCTACGATTCAAACTCCTAAAAATAGGATAGAGTTC
1 TACTACGATTCAAACTCCTAAAAATAGGATAGAATTC
** * *
1705469 TACTATTATTTAAACTCCTAAAGATAGGAT
1 TACTACGATTCAAACTCCTAAAAATAGGAT
1705499 CCACAAGCAT
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.32
Consensus pattern (37 bp):
TACTACGATTCAAACTCCTAAAAATAGGATAGAATTC
Found at i:1706241 original size:22 final size:22
Alignment explanation
Indices: 1706157--1706275 Score: 86
Period size: 22 Copynumber: 5.4 Consensus size: 22
1706147 TTATTTCATT
*
1706157 TATTTATTATTATTATTACTATTTA
1 TATTT-TTATTATT-TTA-TATATA
* *
1706182 CTA-TTTTATTATATTATACATA
1 -TATTTTTATTATTTTATATATA
*
1706204 CATTTTTA-TATTTTTATATATA
1 TATTTTTATTA-TTTTATATATA
*
1706226 TATTTTTATTATTTTATTTATA
1 TATTTTTATTATTTTATATATA
* *
1706248 CTATTTAT-TTATTTT-CAT-TA
1 -TATTTTTATTATTTTATATATA
1706268 TATTTTTA
1 TATTTTTA
1706276 GTTTCTTTGC
Statistics
Matches: 76, Mismatches: 12, Indels: 16
0.73 0.12 0.15
Matches are distributed among these distances:
19 6 0.08
20 2 0.03
21 4 0.05
22 42 0.55
23 11 0.14
24 7 0.09
25 2 0.03
26 2 0.03
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (22 bp):
TATTTTTATTATTTTATATATA
Found at i:1706243 original size:14 final size:14
Alignment explanation
Indices: 1706209--1706275 Score: 59
Period size: 14 Copynumber: 4.8 Consensus size: 14
1706199 ACATACATTT
1706209 TTATATTTTTA-TA
1 TTATATTTTTATTA
1706222 TATATATTTTTATTA
1 T-TATATTTTTATTA
* * *
1706237 TTTTATTTATACTA
1 TTATATTTTTATTA
1706251 TT-TATTTATT-TTCA
1 TTATATTT-TTATT-A
1706265 TTATATTTTTA
1 TTATATTTTTA
1706276 GTTTCTTTGC
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
13 7 0.16
14 28 0.65
15 8 0.19
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (14 bp):
TTATATTTTTATTA
Found at i:1706270 original size:44 final size:43
Alignment explanation
Indices: 1706185--1706274 Score: 103
Period size: 44 Copynumber: 2.1 Consensus size: 43
1706175 CTATTTACTA
*
1706185 TTTTATTATATTATACATACATTTTTATATTTTTATATATATAT
1 TTTTATTATATTATACATACATTTTTATATTTTCATATATAT-T
* **
1706229 TTTTATTATTTTATTTATACTATTTATT-TATTTTCAT-TATATT
1 TTTTATTATATTATACATAC-ATTT-TTATATTTTCATATATATT
1706272 TTT
1 TTT
1706275 AGTTTCTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.10
44 22 0.55
45 12 0.30
46 2 0.05
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (43 bp):
TTTTATTATATTATACATACATTTTTATATTTTCATATATATT
Found at i:1706387 original size:20 final size:19
Alignment explanation
Indices: 1706360--1706415 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1706350 TTTTATCTTC
1706360 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
1706379 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
1706399 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
1706416 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:1711505 original size:3 final size:3
Alignment explanation
Indices: 1711476--1711534 Score: 82
Period size: 3 Copynumber: 19.0 Consensus size: 3
1711466 TTGGGTTTTG
* *
1711476 TAA TAT TAA TAAA TAA TATA TAT TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA
1711523 TAA TAA TAA TAA
1 TAA TAA TAA TAA
1711535 ATTTTAAAAT
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:1712110 original size:113 final size:113
Alignment explanation
Indices: 1711873--1713450 Score: 2724
Period size: 113 Copynumber: 14.0 Consensus size: 113
1711863 AAATTATGCA
* ** * *
1711873 AAAAGGTTGAATAAGCTCTTCTCATTGTGAA---CTT-TTTCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1711934 TATGAACTTCTTT-GGGAAAA-CTGATCCATCA-AGTGATGGATTTGAGC
66 TATGAACTT-TTTCTGGAAAAGCTGATCCATCAGA-TGATGGATTTGAGC
*
1711981 AAAAAGTTGAACAAATTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCA
1 AAAAGGTTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCA
****
1712045 TTATGAACTCAAACTGGAAAAGCTGATCCATCA-AGTGATGGATTTGAGC
65 TTATGAACTTTTTCTGGAAAAGCTGATCCATCAGA-TGATGGATTTGAGC
*
1712094 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCTTTCTTCAGATGATGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTC--A-GATGAGTTCTTCT
* ** * * * * * * * *
1712159 CATTATGAACTCTACCTGGCAATGTTAATCCATCAAATGATGAATTTAAAC
63 CATTATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
* *
1712210 AAAATGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1712275 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
1712323 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1712388 TATGAACTTTTTCTGGAAAAGCTGATCCATTAGATGATGGATTTGAGC
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
*
1712436 AAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1712501 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
1712549 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1712614 TATGAACTTTTTCTGGAAAAGCTGATCCATTAGATGATGGATTTGAGC
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
*
1712662 AAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1712727 TATGAACTTTTTATGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
1712775 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1712840 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
1712888 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1712953 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
*
1713001 AAAAGGTTGAACAAATTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1713066 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
1713114 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
1713179 TATGAACTTTTTCTGGAAAAGCTGATCCATTAGATGATGGATTTGAGC
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
1713227 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1713292 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
* *
1713340 AAAAGGTTGAAAAAATTCTTCTCATTATTAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1713405 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
66 TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGA
1713451 ATCTTTGCTA
Statistics
Matches: 1404, Mismatches: 54, Indels: 19
0.95 0.04 0.01
Matches are distributed among these distances:
108 26 0.02
111 2 0.00
112 43 0.03
113 1232 0.88
114 1 0.00
115 1 0.00
116 98 0.07
117 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.39
Consensus pattern (113 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACTTTTTCTGGAAAAGCTGATCCATCAGATGATGGATTTGAGC
Found at i:1713850 original size:22 final size:22
Alignment explanation
Indices: 1713825--1713879 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
1713815 AATAAAGCTT
1713825 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
1713847 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
1713869 TCATCTTTGAA
1 TCATCTTTGAA
1713880 GAGTGTAGAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:1714377 original size:54 final size:53
Alignment explanation
Indices: 1714251--1714451 Score: 223
Period size: 54 Copynumber: 3.8 Consensus size: 53
1714241 CACTGGTTCA
* * *
1714251 TAAAACATTTGACAATACATTCAT-CTTTTCCTGTGGTTTCTG-TC-GAG-ATG
1 TAAAACATTTGACAACACATTCATCCTTTT-CTGTGGCTTCTGCTCAGAGTTTG
* *
1714301 TAAAACACTTGACAACAGATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGA-GTTTG
* * **
1714355 TAAAACATTTGACAACACATTCATCC-TTTCTTGTGGTTTTTGCTCAGACGTTCA
1 TAAAACATTTGACAACACATTCATCCTTTTC-TGTGGCTTCTGCTCAGA-GTTTG
* * *
1714409 TAAAGCGTTTGACAACACATTCATCCTTTTCTATGGCTTCTGC
1 TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGC
1714452 CAAGATTTCT
Statistics
Matches: 127, Mismatches: 17, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
50 32 0.25
51 7 0.06
52 2 0.02
53 5 0.04
54 77 0.61
55 4 0.03
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (53 bp):
TAAAACATTTGACAACACATTCATCCTTTTCTGTGGCTTCTGCTCAGAGTTTG
Found at i:1714450 original size:108 final size:104
Alignment explanation
Indices: 1714251--1714451 Score: 269
Period size: 104 Copynumber: 1.9 Consensus size: 104
1714241 CACTGGTTCA
* * *
1714251 TAAAACATTTGACAATACATTCATCTTTTCCTGTGGTTTCTGTCGAGATGTAAAACACTTGACAA
1 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTCGAGACGTAAAACACTTGACAA
* *
1714316 CAGATTCATCCTTTTCTGTGGCTTCTGCTCAGATGTTTG
66 CACATTCATCCTTTTCTATGGCTTCTGCTCAGATGTTTG
* * **
1714355 TAAAACATTTGACAACACATTCATCCTTTCTTGTGGTTTTTGCTC-AGACGTTCATAAAGCGTTT
1 TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTG-TCGAGACG-T-A-AAA-CACTT
1714419 GACAACACATTCATCCTTTTCTATGGCTTCTGC
61 GACAACACATTCATCCTTTTCTATGGCTTCTGC
1714452 CAAGATTTCT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
104 42 0.51
105 3 0.04
106 1 0.01
107 3 0.04
108 34 0.41
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (104 bp):
TAAAACATTTGACAACACATTCATCCTTTCCTGTGGTTTCTGTCGAGACGTAAAACACTTGACAA
CACATTCATCCTTTTCTATGGCTTCTGCTCAGATGTTTG
Found at i:1715585 original size:36 final size:34
Alignment explanation
Indices: 1715545--1715618 Score: 78
Period size: 35 Copynumber: 2.1 Consensus size: 34
1715535 CATTACTTCT
*
1715545 TATTG-AGATGAGCCTCCAAAAATGCTCAAATATTC
1 TATTGCAG-TGAGCCTCC-AAAATGCCCAAATATTC
* * *
1715580 ATATTGCTGTGAGCCTTCAAAATGCCCCAATATTC
1 -TATTGCAGTGAGCCTCCAAAATGCCCAAATATTC
1715615 TATT
1 TATT
1715619 TCTGGTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
34 4 0.12
35 15 0.45
36 13 0.39
37 1 0.03
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (34 bp):
TATTGCAGTGAGCCTCCAAAATGCCCAAATATTC
Found at i:1716772 original size:114 final size:114
Alignment explanation
Indices: 1716572--1716912 Score: 565
Period size: 114 Copynumber: 3.0 Consensus size: 114
1716562 GATCATGCAG
* * * * * * *
1716572 TTCATCTTTCAATTCCAATGATCGGTTCTGGGGTTCCTACCGAATCATATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* *
1716637 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
1716686 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
1716751 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTTTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
* *
1716800 TTCATCTTTCAAATCCAATGATTGGTTTTTGGGGTTCATACCAAACTAGATCAGACAACTCAAAG
1 TTCATCTTTCAAATCCAATGATTGG-TTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1716865 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
1716913 CATGGCACTT
Statistics
Matches: 213, Mismatches: 13, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
114 129 0.61
115 84 0.39
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:1719185 original size:7 final size:7
Alignment explanation
Indices: 1719168--1719287 Score: 82
Period size: 7 Copynumber: 15.4 Consensus size: 7
1719158 TTGATTCAAT
1719168 TTTTTTC
1 TTTTTTC
1719175 -TTTTTC
1 TTTTTTC
1719181 TTTTTTC
1 TTTTTTC
1719188 TTTTTTC
1 TTTTTTC
1719195 TTTTTTC
1 TTTTTTC
*
1719202 TTTCTAT-
1 TTT-TTTC
*
1719209 TTCTTTC
1 TTTTTTC
1719216 ATTTTTTTC
1 --TTTTTTC
1719225 ATTTTTTTC
1 --TTTTTTC
1719234 TTTTTTCCTC
1 -TTTTT--TC
1719244 TTTTTTC
1 TTTTTTC
1719251 TTTTTTCC
1 TTTTTT-C
1719259 TTTCTTTGC
1 TTT-TTT-C
1719268 TTGATTTTTC
1 -T--TTTTTC
1719278 TTTTTTC
1 TTTTTTC
1719285 TTT
1 TTT
1719288 CTTTGCTGGA
Statistics
Matches: 96, Mismatches: 5, Indels: 24
0.77 0.04 0.19
Matches are distributed among these distances:
6 8 0.08
7 42 0.44
8 12 0.12
9 25 0.26
10 4 0.04
11 3 0.03
12 2 0.02
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (7 bp):
TTTTTTC
Found at i:1719257 original size:17 final size:17
Alignment explanation
Indices: 1719175--1719259 Score: 70
Period size: 17 Copynumber: 4.9 Consensus size: 17
1719165 AATTTTTTTC
1719175 TTTTTC-TTTTT--TCT
1 TTTTTCTTTTTTCCTCT
*
1719189 TTTTTCTTTTTTCTTTCTAT
1 TTTTTCTTTTTTC---CTCT
*
1719209 TTCTTTCATTTTTTTCAT-T
1 TT-TTTC--TTTTTTCCTCT
1719228 TTTTTCTTTTTTCCTCT
1 TTTTTCTTTTTTCCTCT
1719245 TTTTTCTTTTTTCCT
1 TTTTTCTTTTTTCCT
1719260 TTCTTTGCTT
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
14 6 0.10
15 5 0.09
16 8 0.14
17 16 0.28
18 4 0.07
19 3 0.05
20 5 0.09
21 4 0.07
23 7 0.12
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTTCCTCT
Found at i:1719275 original size:46 final size:47
Alignment explanation
Indices: 1719181--1719285 Score: 114
Period size: 46 Copynumber: 2.3 Consensus size: 47
1719171 TTTCTTTTTC
* **
1719181 TTTTTTC-TTTTT-TCTTTTTTCTTTCTATTTCTTTCATTTTTTTCA
1 TTTTTTCTTTTTTCTCTTTTTTCTTTCTATTCCTTTCATTTGCTTCA
*
1719226 TTTTTTTCTTTTTTCCTCTTTTTTCTTT-T-TTCCTTTC-TTTGCTTGA
1 -TTTTTTCTTTTTT-CTCTTTTTTCTTTCTATTCCTTTCATTTGCTTCA
1719272 -TTTTTCTTTTTTCT
1 TTTTTTCTTTTTTCT
1719286 TTCTTTGCTG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
43 2 0.04
44 12 0.23
46 13 0.25
47 12 0.23
48 1 0.02
49 12 0.23
ACGTcount: A:0.04, C:0.17, G:0.02, T:0.77
Consensus pattern (47 bp):
TTTTTTCTTTTTTCTCTTTTTTCTTTCTATTCCTTTCATTTGCTTCA
Found at i:1719288 original size:26 final size:25
Alignment explanation
Indices: 1719245--1719294 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 25
1719235 TTTTTCCTCT
1719245 TTTTTCTTTTTTCCTTTCTTTGCTTGA
1 TTTTTCTTTTTT-CTTTCTTTGCTT-A
1719272 TTTTTCTTTTTTCTTTCTTTGCT
1 TTTTTCTTTTTTCTTTCTTTGCT
1719295 GGATGAGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.02, C:0.18, G:0.06, T:0.74
Consensus pattern (25 bp):
TTTTTCTTTTTTCTTTCTTTGCTTA
Found at i:1722600 original size:14 final size:14
Alignment explanation
Indices: 1722566--1722619 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
1722556 TTGTGCAATA
* *
1722566 CAAATGCAAAGATG
1 CAAATGTAAATATG
1722580 CCAAATGTAAATATG
1 -CAAATGTAAATATG
*
1722595 CAAATGTAAAAATG
1 CAAATGTAAATATG
*
1722609 TAAATGTAAAT
1 CAAATGTAAAT
1722620 TATTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:1726397 original size:3 final size:3
Alignment explanation
Indices: 1726378--1726431 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
1726368 TTGGGTTTTG
*
1726378 TAA TAT TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1726424 TAA -AA TAA
1 TAA TAA TAA
1726432 AAAAAATTGA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1726437 original size:9 final size:9
Alignment explanation
Indices: 1726384--1726438 Score: 58
Period size: 9 Copynumber: 6.1 Consensus size: 9
1726374 TTTGTAATAT
1726384 TAATAAATAA
1 TAATAAA-AA
*
1726394 TAATAATAA
1 TAATAAAAA
*
1726403 TAATAATAA
1 TAATAAAAA
*
1726412 TAATAATAA
1 TAATAAAAA
1726421 TAAT-AAAA
1 TAATAAAAA
*
1726429 TAAAAAAAA
1 TAATAAAAA
1726438 T
1 T
1726439 TGATGTCTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
8 6 0.15
9 29 0.71
10 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (9 bp):
TAATAAAAA
Found at i:1728291 original size:16 final size:18
Alignment explanation
Indices: 1728259--1728293 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1728249 ATATAAAAAC
1728259 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
1728277 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
1728293 A
1 A
1728294 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:1728329 original size:20 final size:20
Alignment explanation
Indices: 1728304--1728341 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1728294 AATGAGTAAA
1728304 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
1728324 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
1728342 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:1728880 original size:37 final size:37
Alignment explanation
Indices: 1728830--1728918 Score: 97
Period size: 37 Copynumber: 2.4 Consensus size: 37
1728820 GTGCTTGTGA
* * * *
1728830 ATCCTATCTTTAGGAATTTAAATATTAGTAGAACTCT
1 ATCCTATTTTTAGGAATTTAAATACTAGCAAAACTCT
* * * * *
1728867 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAATTTAAATACTAGCAAAACTCT
1728904 ATCCTATTTTTAGGA
1 ATCCTATTTTTAGGA
1728919 TTTTGAATCC
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAATTTAAATACTAGCAAAACTCT
Found at i:1729773 original size:105 final size:105
Alignment explanation
Indices: 1729477--1730138 Score: 922
Period size: 105 Copynumber: 6.3 Consensus size: 105
1729467 GCATTGTTCT
* * *** *
1729477 GAGTCCAATATCCTCCGTTGTGAAGTTAAAATTGGCTCTG-GAACCAGGAAATTGTTTGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACA
* * * * *
1729541 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * ** *
1729583 GAGTCCAATATCCTTCGCTGTGCAGTTGAAATTGATTCTGA-A-T--GAAATT-TTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
1729643 CAGCGGTCCCTTCGTCGTGGAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
1729683 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGTGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1729748 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
1729788 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
*
1729853 CAGCAGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
1729893 AAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
* *
1729958 CAGCGGTCCCTTCGTCGAGAAGTTGAACTTGCATTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
1729998 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAA
* * * *
1730063 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT-G
* * *
1730105 AGTGTCACAATATCCTCCGTTGTGGAGTTGAAAT
1 -GAGTC-CAATATCCTTCGTTGTGAAGTTGAAAT
1730139 CGCGGATGTT
Statistics
Matches: 506, Mismatches: 40, Indels: 17
0.90 0.07 0.03
Matches are distributed among these distances:
100 80 0.16
101 1 0.00
102 7 0.01
104 5 0.01
105 305 0.60
106 78 0.15
107 1 0.00
108 4 0.01
109 25 0.05
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAG
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:1730354 original size:36 final size:36
Alignment explanation
Indices: 1730307--1730382 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
1730297 TGTTTGGAGA
* *
1730307 GAAACTGTCTCAAGGGAGACAAAATTCGTTTCAAGG
1 GAAACTATCTCAAGGGAGACAAAATTCATTTCAAGG
* *
1730343 GAAACTATCTCAAGTGAGATAAAATTCATTTCAAGG
1 GAAACTATCTCAAGGGAGACAAAATTCATTTCAAGG
1730379 GAAA
1 GAAA
1730383 TGTTTTCAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
GAAACTATCTCAAGGGAGACAAAATTCATTTCAAGG
Found at i:1730503 original size:106 final size:104
Alignment explanation
Indices: 1730282--1730600 Score: 479
Period size: 106 Copynumber: 3.1 Consensus size: 104
1730272 TTCGTTAAAT
* ** *
1730282 TGTTTTCAAAGTTTATGTTTGGAGAGAAACTGTCTCAAGGGAGACAAAA--TTC-GTTTCAAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
1730344 AAACTATCTCAAGTGAG-ATAAAATTCATTTCAAGGGAAA
66 AAACTATCTCAAG-GAGAAAAAAATTCATTTCAAGGGAAA
1730383 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
* *
1730448 AAACTATCTCAAGAGAGAAAAAAAAATCATTTCAAGAGAAA
66 AAACTATCTCAAG-GAG-AAAAAAATTCATTTCAAGGGAAA
*
1730489 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAATTTTCTGTTTCGAGGG
1 TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
*
1730554 -AACTATCTC-AGGAGAGAAAAAATTAATTTCAAGGGAAA
66 AAACTATCTCAAGGAGA-AAAAAATTCATTTCAAGGGAAA
1730592 TGTTTTCAA
1 TGTTTTCAA
1730601 GAGAAACTGT
Statistics
Matches: 200, Mismatches: 12, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
101 46 0.23
102 1 0.00
103 34 0.17
104 27 0.14
105 9 0.05
106 83 0.41
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (104 bp):
TGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTCTGTTTCGAGGG
AAACTATCTCAAGGAGAAAAAAATTCATTTCAAGGGAAA
Found at i:1730757 original size:36 final size:36
Alignment explanation
Indices: 1730717--1730830 Score: 122
Period size: 36 Copynumber: 3.2 Consensus size: 36
1730707 CTTTCGAGTG
* *
1730717 AAAACGGTCTCAAGCGAGACAAATATTGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAATATTGTTTTAAGA
* ** * * * * *
1730753 AAAACAATCTTGAGTGAAATAAATCTTCTTTCAAGA
1 AAAACAGTCTCAAGTGAGACAAATATTGTTTTAAGA
1730789 AAAACAGTCTCAAGTGAGACAAAGTA-TGTTTTAAGA
1 AAAACAGTCTCAAGTGAGACAAA-TATTGTTTTAAGA
1730825 AAAACA
1 AAAACA
1730831 AATTTGAGTG
Statistics
Matches: 59, Mismatches: 18, Indels: 2
0.75 0.23 0.03
Matches are distributed among these distances:
36 58 0.98
37 1 0.02
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (36 bp):
AAAACAGTCTCAAGTGAGACAAATATTGTTTTAAGA
Found at i:1730819 original size:72 final size:74
Alignment explanation
Indices: 1730671--1730846 Score: 216
Period size: 72 Copynumber: 2.4 Consensus size: 74
1730661 TAAAATCTTC
* ** * * *
1730671 TTAAAAAAAACAGCCTTGAGTGAAATAAAATGCCTTCTTTCGAGTGAAAACGGTCTCAAGCGAGA
1 TTAAGAAAAACAATCTTGAGTGAAAT-AAAT-CCTTCTTTCAAGTAAAAACAGTCTCAAGCGAGA
1730736 CAAATATTGTT
64 CAAATATTGTT
*
1730747 TTAAGAAAAACAATCTTGAGTGAAATAAAT-CTTCTTTCAAG-AAAAACAGTCTCAAGTGAGACA
1 TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCAAGTAAAAACAGTCTCAAGCGAGACA
1730810 AAGTA-TGTT
66 AA-TATTGTT
*
1730819 TTAAGAAAAACAAAT-TTGAGTGAGATAA
1 TTAAGAAAAAC-AATCTTGAGTGAAATAA
1730847 TCATCTGCAT
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
72 48 0.53
73 15 0.17
75 4 0.04
76 23 0.26
ACGTcount: A:0.44, C:0.12, G:0.17, T:0.27
Consensus pattern (74 bp):
TTAAGAAAAACAATCTTGAGTGAAATAAATCCTTCTTTCAAGTAAAAACAGTCTCAAGCGAGACA
AATATTGTT
Found at i:1730841 original size:36 final size:35
Alignment explanation
Indices: 1730732--1730843 Score: 111
Period size: 36 Copynumber: 3.1 Consensus size: 35
1730722 GGTCTCAAGC
1730732 GAGACAAATATTGTTTTAAGAAAAACAATCTTGAGT
1 GAGACAAATA-TGTTTTAAGAAAAACAATCTTGAGT
* * * * **
1730768 GAAATAAATCT-TCTTTCAAGAAAAACAGTCTCAAGT
1 GAGACAAATATGT-TTT-AAGAAAAACAATCTTGAGT
1730804 GAGACAAAGTATGTTTTAAGAAAAACAAAT-TTGAGT
1 GAGACAAA-TATGTTTTAAGAAAAAC-AATCTTGAGT
1730840 GAGA
1 GAGA
1730844 TAATCATCTG
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
34 1 0.02
35 4 0.07
36 46 0.78
37 7 0.12
38 1 0.02
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.28
Consensus pattern (35 bp):
GAGACAAATATGTTTTAAGAAAAACAATCTTGAGT
Found at i:1732272 original size:183 final size:183
Alignment explanation
Indices: 1731964--1732500 Score: 959
Period size: 183 Copynumber: 2.9 Consensus size: 183
1731954 ATCAGGTTTA
* * *
1731964 ACTGAAGGGTTCATCTCATCATAAAGTATTTGACCTGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
* **
1732029 GCCAAGTGTCCGAGCAATGTCAT-GATTTGAATGTAATCTATTCATAAAGCCAGGGCTTTCGAGT
66 GCCAAGTGTCCGAGCAGTGTCATAG-TTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGT
1732093 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
130 TTCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
* * *
1732147 ACTGAAGGGTTCGTCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAACAAACACCAAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1732212 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
*
1732277 TCCTCTATAACCAATAGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
*
1732330 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCATGACAAAAGCAGTGGAGCAAACACCGAATT
1 ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
1732395 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
66 GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
1732460 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
131 TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTA
1732501 CGGATTTAAT
Statistics
Matches: 338, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
183 337 1.00
184 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (183 bp):
ACTGAAGGGTTCATCTCATCACAAAGTCTTTGGCCTGACAAAAGCAGTGGAGCAAACACCGAATT
GCCAAGTGTCCGAGCAGTGTCATAGTTTGAACATAATCTATTCATAAAGCCAGGGCTTTCGAGTT
TCCTCTATAACCAATTGCCTTAGTGGAATAGCTCAGCTTTAGAGGGACAAATC
Found at i:1737945 original size:16 final size:18
Alignment explanation
Indices: 1737913--1737947 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
1737903 ATATAAAAAC
1737913 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
1737931 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
1737947 A
1 A
1737948 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:1737959 original size:22 final size:20
Alignment explanation
Indices: 1737925--1737967 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
1737915 AAAATATAGG
1737925 ATAAATATAAAAATAGATAA
1 ATAAATATAAAAATAGATAA
*
1737945 ATAAATGAGTAAAAATATATAA
1 ATAAAT-A-TAAAAATAGATAA
1737967 A
1 A
1737968 AAAGTAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 1 0.05
22 13 0.65
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
ATAAATATAAAAATAGATAA
Found at i:1737973 original size:18 final size:19
Alignment explanation
Indices: 1737952--1737996 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1737942 TAAATAAATG
1737952 AGTAAAA-ATATATAAAAA
1 AGTAAAACATATATAAAAA
* *
1737970 AGTAAAAGCATATATATATA
1 AGTAAAA-CATATATAAAAA
1737990 AGTAAAA
1 AGTAAAA
1737997 TAATAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 7 0.30
20 16 0.70
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.24
Consensus pattern (19 bp):
AGTAAAACATATATAAAAA
Found at i:1737984 original size:20 final size:20
Alignment explanation
Indices: 1737959--1737996 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1737949 ATGAGTAAAA
1737959 ATATATAAAAAAGTAAAAGC
1 ATATATAAAAAAGTAAAAGC
* *
1737979 ATATATATATAAGTAAAA
1 ATATATAAAAAAGTAAAA
1737997 TAATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (20 bp):
ATATATAAAAAAGTAAAAGC
Found at i:1738065 original size:2 final size:2
Alignment explanation
Indices: 1738058--1738086 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1738048 AAAATAGGAA
1738058 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 A
1738087 ATAACACTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1738551 original size:37 final size:37
Alignment explanation
Indices: 1738501--1738605 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
1738491 GTGCTTGTGG
* * *
1738501 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTATTTTTAGGAATTTGAATCCTAGTAGAACTCT
* * * * *
1738538 ATCCTATTTTTAGGAGTTTGAATCCTAGCAAAATTTT
1 ATCCTATTTTTAGGAATTTGAATCCTAGTAGAACTCT
*
1738575 ATCCTATTTTTAGGATTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAATTTGAATCCTAGTAG
1738606 GACGAAAATG
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAGGAATTTGAATCCTAGTAGAACTCT
Found at i:1741097 original size:31 final size:31
Alignment explanation
Indices: 1741009--1741134 Score: 121
Period size: 31 Copynumber: 4.0 Consensus size: 31
1740999 GAACCTCGGC
* * *
1741009 AACTGTCCATAGGTCCCGAAGAACCTAGGTA
1 AACTGTCCATATGTCTCGAAGAACATAGGTA
* **
1741040 AACTATCCATATGT-TCTTTAGAACATAGGTA
1 AACTGTCCATATGTCTC-GAAGAACATAGGTA
* * *
1741071 AACTGTCTATATGTCTCGAAGGACATACGTA
1 AACTGTCCATATGTCTCGAAGAACATAGGTA
*
1741102 ATCCTGTCCATATGTCTCGAA-AGACATAGGTA
1 A-ACTGTCCATATGTCTCGAAGA-ACATAGGTA
1741134 A
1 A
1741135 CCCTCGACTC
Statistics
Matches: 75, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
30 1 0.01
31 46 0.61
32 28 0.37
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (31 bp):
AACTGTCCATATGTCTCGAAGAACATAGGTA
Found at i:1741115 original size:32 final size:32
Alignment explanation
Indices: 1741073--1741134 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
1741063 CATAGGTAAA
* *
1741073 CTGTCTATATGTCTCGAAGGACATACGTAATC
1 CTGTCCATATGTCTCGAAAGACATACGTAATC
*
1741105 CTGTCCATATGTCTCGAAAGACATAGGTAA
1 CTGTCCATATGTCTCGAAAGACATACGTAA
1741135 CCCTCGACTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (32 bp):
CTGTCCATATGTCTCGAAAGACATACGTAATC
Done.