Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6
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: 4312818
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 226954 characters in sequence are not A, C, G, or T
File 11 of 14
Found at i:3390665 original size:27 final size:27
Alignment explanation
Indices: 3390635--3390711 Score: 127
Period size: 27 Copynumber: 2.9 Consensus size: 27
3390625 AAAAAACCTG
*
3390635 TGGCGGCACCAAAGGTGCCAAAGAAAT
1 TGGCGGCACCAATGGTGCCAAAGAAAT
*
3390662 TGGCGGCACCAATGGTGCCAAAGAGAT
1 TGGCGGCACCAATGGTGCCAAAGAAAT
*
3390689 TGGGGGCACCAATGGTGCCAAAG
1 TGGCGGCACCAATGGTGCCAAAG
3390712 GACTAAAATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.31, C:0.22, G:0.34, T:0.13
Consensus pattern (27 bp):
TGGCGGCACCAATGGTGCCAAAGAAAT
Found at i:3391567 original size:16 final size:16
Alignment explanation
Indices: 3391546--3391577 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3391536 GGTGCCGCCA
*
3391546 CAGGTTTTTTTTTTTG
1 CAGGTTTTTGTTTTTG
3391562 CAGGTTTTTGTTTTTG
1 CAGGTTTTTGTTTTTG
3391578 GTAAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.06, G:0.22, T:0.66
Consensus pattern (16 bp):
CAGGTTTTTGTTTTTG
Found at i:3392333 original size:18 final size:17
Alignment explanation
Indices: 3392310--3392343 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3392300 TTTTCTTAAA
3392310 AAAATTCTATCTTTTGAC
1 AAAATTC-ATCTTTTGAC
*
3392328 AAAATTCGTCTTTTGA
1 AAAATTCATCTTTTGA
3392344 TTTTTTAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (17 bp):
AAAATTCATCTTTTGAC
Found at i:3418421 original size:22 final size:22
Alignment explanation
Indices: 3418393--3418461 Score: 111
Period size: 22 Copynumber: 3.1 Consensus size: 22
3418383 TATGCACTAT
*
3418393 TAAACAGAGAGCACTAAAGTGC
1 TAAACAGAGAGCACTAATGTGC
* *
3418415 TATACAGAGAGCACGAATGTGC
1 TAAACAGAGAGCACTAATGTGC
3418437 TAAACAGAGAGCACTAATGTGC
1 TAAACAGAGAGCACTAATGTGC
3418459 TAA
1 TAA
3418462 TAATCGGAGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.17
Consensus pattern (22 bp):
TAAACAGAGAGCACTAATGTGC
Found at i:3418479 original size:19 final size:19
Alignment explanation
Indices: 3418455--3418492 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3418445 GAGCACTAAT
*
3418455 GTGCTAATAATCGGAGAGC
1 GTGCTAATAATCAGAGAGC
*
3418474 GTGCTAGTAATCAGAGAGC
1 GTGCTAATAATCAGAGAGC
3418493 ACTAACGTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.32, T:0.21
Consensus pattern (19 bp):
GTGCTAATAATCAGAGAGC
Found at i:3418501 original size:25 final size:24
Alignment explanation
Indices: 3418397--3418579 Score: 163
Period size: 25 Copynumber: 7.8 Consensus size: 24
3418387 CACTATTAAA
*
3418397 CAGAGAGCACTAAAGTGCTAT-A-
1 CAGAGAGCACTAACGTGCTATAAT
* *
3418419 CAGAGAGCACGAATGTGCTA-AA-
1 CAGAGAGCACTAACGTGCTATAAT
*
3418441 CAGAGAGCACTAATGTGCTAATAAT
1 CAGAGAGCACTAACGTGCT-ATAAT
*
3418466 C-G-GAG----AGCGTGCTAGTAAT
1 CAGAGAGCACTAACGTGCTA-TAAT
3418485 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACTAACGTGCT-ATAAT
3418510 CAGAGAGCAC-AGACGTGCTAGTAAT
1 CAGAGAGCACTA-ACGTGCTA-TAAT
* *
3418535 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACTAACGTGCTATA-AT
*
3418560 CAGAGAGCACCAACGTGCTA
1 CAGAGAGCACTAACGTGCTA
3418580 AGTGCTAAAT
Statistics
Matches: 135, Mismatches: 10, Indels: 29
0.78 0.06 0.17
Matches are distributed among these distances:
18 1 0.01
19 11 0.08
20 1 0.01
21 3 0.02
22 37 0.27
23 4 0.03
24 6 0.04
25 71 0.53
26 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.25, T:0.18
Consensus pattern (24 bp):
CAGAGAGCACTAACGTGCTATAAT
Found at i:3418532 original size:50 final size:50
Alignment explanation
Indices: 3418397--3418626 Score: 211
Period size: 50 Copynumber: 4.7 Consensus size: 50
3418387 CACTATTAAA
* *
3418397 CAGAGAGCACTAAAGTGCT-AT-A-CAGAGAGCAC-GAATGTGCTA--AA-
1 CAGAGAGCACTAACGTGCTAATAATCAGAGAGCACAG-ACGTGCTAGTAAT
*
3418441 CAGAGAGCACTAATGTGCTAATAATC-G-GAG---AG-CGTGCTAGTAAT
1 CAGAGAGCACTAACGTGCTAATAATCAGAGAGCACAGACGTGCTAGTAAT
3418485 CAGAGAGCACTAACGTGCTAATAATCAGAGAGCACAGACGTGCTAGTAAT
1 CAGAGAGCACTAACGTGCTAATAATCAGAGAGCACAGACGTGCTAGTAAT
*
3418535 CAGAGAGCACTGACGTGCTAA-ATATCAGAGAGCACCA-ACGTGCTAAGTGCTAAATAT
1 CAGAGAGCACTAACGTGCTAATA-ATCAGAGAGCA-CAGACGTGCT-A--G-T--A-AT
* *
3418592 CAGAGAGCACTGATGTGCTAATAATCAGAGAGCAC
1 CAGAGAGCACTAACGTGCTAATAATCAGAGAGCAC
3418627 GCTAAACTCC
Statistics
Matches: 158, Mismatches: 5, Indels: 34
0.80 0.03 0.17
Matches are distributed among these distances:
41 6 0.04
43 3 0.02
44 43 0.27
45 6 0.04
46 5 0.03
47 1 0.01
49 3 0.02
50 50 0.32
51 3 0.02
53 1 0.01
54 1 0.01
56 2 0.01
57 33 0.21
58 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (50 bp):
CAGAGAGCACTAACGTGCTAATAATCAGAGAGCACAGACGTGCTAGTAAT
Found at i:3418580 original size:25 final size:25
Alignment explanation
Indices: 3418397--3418626 Score: 146
Period size: 25 Copynumber: 9.4 Consensus size: 25
3418387 CACTATTAAA
* *
3418397 CAGAGAGCACTAAAGTGCT-AT-A-
1 CAGAGAGCACCAACGTGCTAATAAT
* *
3418419 CAGAGAGCACGAATGTGCT-A-AA-
1 CAGAGAGCACCAACGTGCTAATAAT
* *
3418441 CAGAGAGCACTAATGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
* *
3418466 C-G-GAG----AGCGTGCTAGTAAT
1 CAGAGAGCACCAACGTGCTAATAAT
*
3418485 CAGAGAGCACTAACGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
*
3418510 CAGAGAGCA-CAGACGTGCTAGTAAT
1 CAGAGAGCACCA-ACGTGCTAATAAT
**
3418535 CAGAGAGCACTGACGTGCTAA-ATAT
1 CAGAGAGCACCAACGTGCTAATA-AT
3418560 CAGAGAGCACCAACGTGCTAAGTGCTAAATAT
1 CAGAGAGCACCAACGTGCTAA----T--A-AT
** *
3418592 CAGAGAGCACTGATGTGCTAATAAT
1 CAGAGAGCACCAACGTGCTAATAAT
3418617 CAGAGAGCAC
1 CAGAGAGCAC
3418627 GCTAAACTCC
Statistics
Matches: 170, Mismatches: 18, Indels: 37
0.76 0.08 0.16
Matches are distributed among these distances:
19 12 0.07
20 1 0.01
21 3 0.02
22 37 0.22
23 4 0.02
24 5 0.03
25 84 0.49
26 1 0.01
28 1 0.01
32 22 0.13
ACGTcount: A:0.37, C:0.19, G:0.25, T:0.19
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTAATAAT
Found at i:3428383 original size:20 final size:20
Alignment explanation
Indices: 3428339--3428402 Score: 67
Period size: 20 Copynumber: 3.1 Consensus size: 20
3428329 TCTTAGATTT
* *
3428339 TTATGTTTTATATATATTATT
1 TTATGTTATA-ATATATTATA
*
3428360 TTAT-TATATAATATAATATA
1 TTATGT-TATAATATATTATA
*
3428380 TTATGTTATATTATATTATA
1 TTATGTTATAATATATTATA
3428400 TTA
1 TTA
3428403 AATAAACTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 28 0.78
21 8 0.22
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (20 bp):
TTATGTTATAATATATTATA
Found at i:3428388 original size:5 final size:5
Alignment explanation
Indices: 3428346--3428402 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
3428336 TTTTTATGTT
* *
3428346 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATG TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
3428395 TTATA TTA
1 TTATA TTA
3428403 AATAAACTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.19
5 30 0.70
7 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:3433366 original size:24 final size:25
Alignment explanation
Indices: 3433282--3433367 Score: 88
Period size: 24 Copynumber: 3.5 Consensus size: 25
3433272 GCTTATCCGG
* *
3433282 GCAATATAACGGGAAGCTCACAAAGA
1 GCAATATAACGGGTAGCTC-CGAAGA
* * * *
3433308 GC-CTATAACGAGTAACTCTGAAGA
1 GCAATATAACGGGTAGCTCCGAAGA
3433332 GCAAT-TAACGGGTAGCTCCGAAGA
1 GCAATATAACGGGTAGCTCCGAAGA
3433356 GCAAT-TAACGGG
1 GCAATATAACGGG
3433368 AAGTTCAAGC
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
24 34 0.69
25 13 0.27
26 2 0.04
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (25 bp):
GCAATATAACGGGTAGCTCCGAAGA
Found at i:3433923 original size:21 final size:21
Alignment explanation
Indices: 3433897--3433942 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3433887 TATATGAGTA
* *
3433897 AATTTAGAATCAATTTAATAC
1 AATTTACAATCAATTCAATAC
* *
3433918 AATTTACATTCAATTCAATCC
1 AATTTACAATCAATTCAATAC
3433939 AATT
1 AATT
3433943 CACATCTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.39
Consensus pattern (21 bp):
AATTTACAATCAATTCAATAC
Found at i:3433947 original size:21 final size:21
Alignment explanation
Indices: 3433906--3433947 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3433896 AAATTTAGAA
* *
3433906 TCAATTTAATACAATTTACAT
1 TCAATTCAATACAATTCACAT
*
3433927 TCAATTCAATCCAATTCACAT
1 TCAATTCAATACAATTCACAT
3433948 CTTAGACAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.21, G:0.00, T:0.38
Consensus pattern (21 bp):
TCAATTCAATACAATTCACAT
Found at i:3439127 original size:18 final size:18
Alignment explanation
Indices: 3439100--3439135 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3439090 GGCCCCAGCG
* *
3439100 ATGGGGATGGGGATGGGT
1 ATGGGCATGGGCATGGGT
3439118 ATGGGCATGGGCATGGGT
1 ATGGGCATGGGCATGGGT
3439136 GTCATGGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.06, G:0.56, T:0.22
Consensus pattern (18 bp):
ATGGGCATGGGCATGGGT
Found at i:3443894 original size:3 final size:3
Alignment explanation
Indices: 3443544--3443875 Score: 655
Period size: 3 Copynumber: 110.7 Consensus size: 3
3443534 TTGCATTTTG
*
3443544 AAT AAA AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3443592 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3443640 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3443688 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3443736 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3443784 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3443832 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
3443876 ATATAGCAGA
Statistics
Matches: 327, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
3 327 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3444522 original size:19 final size:19
Alignment explanation
Indices: 3444498--3444535 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3444488 TTTGAGCAAC
3444498 AAAAAATAA-ATAAAAAATT
1 AAAAAA-AAGATAAAAAATT
*
3444517 AAAAAAAAGATAACAAATT
1 AAAAAAAAGATAAAAAATT
3444536 CCTTAAAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAAAAAAGATAAAAAATT
Found at i:3445509 original size:45 final size:44
Alignment explanation
Indices: 3445458--3445549 Score: 112
Period size: 44 Copynumber: 2.1 Consensus size: 44
3445448 TAAGACTTAT
* ** *
3445458 ATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTTTCTTTG
1 ATCTACTTCA-CACCAATACAGGAAGACAAGATCTGCTTTCTTCG
* * *
3445503 ATCTACTTCACGCCAATACATGAAGACAATATCTGCTTTCTTCG
1 ATCTACTTCACACCAATACAGGAAGACAAGATCTGCTTTCTTCG
3445547 ATC
1 ATC
3445550 GATTCCACTG
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 30 0.75
45 10 0.25
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (44 bp):
ATCTACTTCACACCAATACAGGAAGACAAGATCTGCTTTCTTCG
Found at i:3445745 original size:131 final size:131
Alignment explanation
Indices: 3445551--3446228 Score: 1034
Period size: 132 Copynumber: 5.2 Consensus size: 131
3445541 TCTTCGATCG
* * * * * * *
3445551 ATTCCACTGCCGACCGGGGAAATAGAATTACTGGCTTCAATATACTCCACTGCAACCTCAGGGAG
1 ATTCCACTGCTGCCCAGGGAAA-AGGATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
*** * * *
3445616 GTAAAATATGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCCTCAAT
65 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAAT
3445681 CT
130 CT
3445683 ATTCCACTGCTGCCCAGGGAAAAGGATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGG
1 ATTCCACTGCTGCCCAGGGAAAAGGATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGG
*
3445748 TAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTATGGAGATAAGATCTGTTATCTTTAATC
66 TAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATC
3445813 T
131 T
3445814 ATTCCACTGCTGCCCAGGGAAAAGGATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGG
1 ATTCCACTGCTGCCCAGGGAAAAGGATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGG
* *
3445879 TAAAATCCACCATCTTTGATCTGCTCCTCTATTGCTTAGGGAGATAAGATCTGTTATCTTTAATC
66 TAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATC
3445944 T
131 T
* *
3445945 ATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
1 ATTCCACTGCTGCCCAGGGA-AAAGGATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
* * * *
3446010 GTAAAATCCACCATCTTTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTGTAATCCTCAAT
65 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAAT
*
3446075 AT
130 CT
** * **
3446077 ATTCCACTGCTGCCCAGGGAGTA-GAGTTACTTGGCTTCAATATACTCCACTACAACCTCAGGGA
1 ATTCCACTGCTGCCCAGGGAAAAGGA-TTA-TTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
** *
3446141 GGTAAAATCTGCCATCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTTATCTTTAA
64 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAA
3446206 TCT
129 TCT
3446209 ATTCCACTGCTGCCCAGGGA
1 ATTCCACTGCTGCCCAGGGA
3446229 GATAAGATCT
Statistics
Matches: 506, Mismatches: 37, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
130 1 0.00
131 251 0.50
132 254 0.50
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (131 bp):
ATTCCACTGCTGCCCAGGGAAAAGGATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGG
TAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAATC
T
Found at i:3445964 original size:44 final size:44
Alignment explanation
Indices: 3445628--3446408 Score: 302
Period size: 44 Copynumber: 17.8 Consensus size: 44
3445618 AAAATATGCC
* * * ** *
3445628 ATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTA
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTT
* * * *
3445672 ATCCTCAATCTATTCCACTGCTGCCCAGGGA-A-AAGGAT-TATT
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAA-GATCTGTT
** * * * * * ****
3445714 GGCTTCAATGTACTCCACTG-TAACCTCAGGGAGGTAAAATCCACC
1 ATCTTTAATCTACTCCACTGCT-GCC-CAGGGAGATAAGATCTGTT
* * * ** *
3445759 ATCTTTGATCTGCTCCACTACTGCTTATGGAGATAAGATCTGTT
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTT
* *
3445803 ATCTTTAATCTATTCCACTGCTGCCCAGGGA-A-AAGGAT-TATT
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAA-GATCTGTT
** * * * * * ****
3445845 GGCTTCAATGTACTCCACTG-TAACCTCAGGGAGGTAAAATCCACC
1 ATCTTTAATCTACTCCACTGCT-GCC-CAGGGAGATAAGATCTGTT
* * * ** **
3445890 ATCTTTGATCTGCTCCTCTATTGCTTAGGGAGATAAGATCTGTT
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTT
* *
3445934 ATCTTTAATCTATTCCACTGCTGCCCAGGGAGAT-AGAAT-TATT
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAG-ATCTGTT
** * * * * * ****
3445977 GGCTTCAATGTACTCCACTG-TAACCTCAGGGAGGTAAAATCCACC
1 ATCTTTAATCTACTCCACTGCT-GCC-CAGGGAGATAAGATCTGTT
* * * * ** *
3446022 ATCTTTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTGTA
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTT
* * * * *
3446066 ATCCTCAATATATTCCACTGCTGCCCAGGGAG-T-AGAGT-TACTT
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGA-TCT-GTT
** * * * ** * * **
3446109 GGCTTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTGCC
1 ATCTTTAATCTACTCCACTGCTGCC-CAGGGAGATAAGATCTGTT
* * * * **
3446154 ATCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTT
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTT
* *
3446198 ATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAAGATCTGTA
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTT
* * *
3446242 ATCCTCAATCTATTCCACTGCTGCCCAGGGAGAT-AGA---GTT
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTT
* * * ** * * **
3446282 AATGGCTTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTGCC
1 -AT--CTTTAATCTACTCCACTGCTGCC-CAGGGAGATAAGATCTGTT
* * * * **
3446330 ATCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTT
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTT
*
3446374 ATCTTTAATCTATTCCACTGCTGCCCAGGGAGATA
1 ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATA
3446409 GAATTATTGG
Statistics
Matches: 517, Mismatches: 186, Indels: 68
0.67 0.24 0.09
Matches are distributed among these distances:
40 2 0.00
41 4 0.01
42 48 0.09
43 83 0.16
44 285 0.55
45 86 0.17
46 6 0.01
47 2 0.00
48 1 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCTTTAATCTACTCCACTGCTGCCCAGGGAGATAAGATCTGTT
Found at i:3446036 original size:132 final size:132
Alignment explanation
Indices: 3445551--3446232 Score: 1046
Period size: 131 Copynumber: 5.2 Consensus size: 132
3445541 TCTTCGATCG
* * * * * * *
3445551 ATTCCACTGCCGACCGGGGAAATAGAATTACTGGCTTCAATATACTCCACTGCAACCTCAGGGAG
1 ATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
*** * * *
3445616 GTAAAATATGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATCCTCAAT
66 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAAT
3445681 CT
131 CT
* *
3445683 ATTCCACTGCTGCCCAGGGA-AAAGGATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
1 ATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
*
3445747 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTATGGAGATAAGATCTGTTATCTTTAAT
66 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAAT
3445812 CT
131 CT
* *
3445814 ATTCCACTGCTGCCCAGGGA-AAAGGATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
1 ATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
* *
3445878 GTAAAATCCACCATCTTTGATCTGCTCCTCTATTGCTTAGGGAGATAAGATCTGTTATCTTTAAT
66 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAAT
3445943 CT
131 CT
3445945 ATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
1 ATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
* * * *
3446010 GTAAAATCCACCATCTTTGATCTGCTCCTCTACTGCTTAGGGAGATAAGATCTGTAATCCTCAAT
66 GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAAT
*
3446075 AT
131 CT
* * **
3446077 ATTCCACTGCTGCCCAGGGAG-TAGAGTTACTTGGCTTCAATATACTCCACTACAACCTCAGGGA
1 ATTCCACTGCTGCCCAGGGAGATAGAATTA-TTGGCTTCAATGTACTCCACTGTAACCTCAGGGA
** *
3446141 GGTAAAATCTGCCATCTTTGATCTGCTCCACTACTACTTAGGGAGATAAGATCTGTTATCTTTAA
65 GGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAA
3446206 TCT
130 TCT
3446209 ATTCCACTGCTGCCCAGGGAGATA
1 ATTCCACTGCTGCCCAGGGAGATA
3446233 AGATCTGTAA
Statistics
Matches: 510, Mismatches: 37, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
131 254 0.50
132 254 0.50
133 2 0.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (132 bp):
ATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCTTCAATGTACTCCACTGTAACCTCAGGGAG
GTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTTATCTTTAAT
CT
Found at i:3446259 original size:176 final size:176
Alignment explanation
Indices: 3446048--3446408 Score: 688
Period size: 176 Copynumber: 2.1 Consensus size: 176
3446038 TCTACTGCTT
*
3446048 AGGGAGATAAGATCTGTAATCCTCAATATATTCCACTGCTGCCCAGGGAG-TAGAGTTACTTGGC
1 AGGGAGATAAGATCTGTAATCCTCAATATATTCCACTGCTGCCCAGGGAGATAGAGTTA-ATGGC
3446112 TTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTA
65 TTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTA
3446177 CTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
130 CTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
*
3446224 AGGGAGATAAGATCTGTAATCCTCAATCTATTCCACTGCTGCCCAGGGAGATAGAGTTAATGGCT
1 AGGGAGATAAGATCTGTAATCCTCAATATATTCCACTGCTGCCCAGGGAGATAGAGTTAATGGCT
3446289 TCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTAC
66 TCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTAC
3446354 TTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
131 TTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
3446400 AGGGAGATA
1 AGGGAGATA
3446409 GAATTATTGG
Statistics
Matches: 182, Mismatches: 2, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
176 174 0.96
177 8 0.04
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (176 bp):
AGGGAGATAAGATCTGTAATCCTCAATATATTCCACTGCTGCCCAGGGAGATAGAGTTAATGGCT
TCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTAC
TTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
Found at i:3446316 original size:132 final size:131
Alignment explanation
Indices: 3446166--3446514 Score: 464
Period size: 132 Copynumber: 2.6 Consensus size: 131
3446156 CTTTGATCTG
* * * * ** * ** * **
3446166 CTCCACTACTACTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCCAGGGAGA
1 CTCCACTACAACTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGA
* *
3446231 TAAGATCTGTAATCCTCAATCTATTCCACTGCTGCCCAGGGAGATAGAGTTAATGGCTTCAATAT
66 TAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTAATGGCTTCAATAT
3446296 A
131 A
*
3446297 CTCCACTACAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTACTTAGGGAG
1 CTCCACTACAA-CTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
* * * *
3446362 ATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCTTCAATG
65 ATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTAATGGCTTCAATA
3446427 TA
130 TA
** **
3446429 CTCCACTGTAATCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
1 CTCCACTACAA-CTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAG
*
3446494 ACAAGATCTGTAATCTTCAAT
65 ATAAGATCTGTAATCTTCAAT
3446515 TTGTTCAACT
Statistics
Matches: 189, Mismatches: 28, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
131 10 0.05
132 179 0.95
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (131 bp):
CTCCACTACAACTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGA
TAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTAATGGCTTCAATAT
A
Found at i:3446474 original size:308 final size:308
Alignment explanation
Indices: 3445916--3446510 Score: 940
Period size: 308 Copynumber: 1.9 Consensus size: 308
3445906 TCTATTGCTT
* * * *
3445916 AGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTATTGGCT
1 AGGGAGATAAGATCTGTAATCCTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTAATGGCT
* ** * *
3445981 TCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCTCTACTGC
66 TCAATATACTCCACTACAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTAC
*
3446046 TTAGGGAGATAAGATCTGTAATCCTCAATATATTCCACTGCTGCCCAGGGAGTAGAGTTACTTGG
131 TTAGGGAGATAAGATCTGTAATCCTCAATATATTCCACTGCTGCCCAGGGAGTAGAATTACTTGG
**
3446111 CTTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACT
196 CTTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACT
* *
3446176 ACTTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCC
261 ACTTAGGGAGACAAGATCTGTAATCTTTAATCTATTCCACTGCTGCCC
*
3446224 AGGGAGATAAGATCTGTAATCCTCAATCTATTCCACTGCTGCCCAGGGAGATAGAGTTAATGGCT
1 AGGGAGATAAGATCTGTAATCCTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTAATGGCT
**
3446289 TCAATATACTCCACTACAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTAC
66 TCAATATACTCCACTACAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTAC
* * * *
3446354 TTAGGGAGATAAGATCTGTTATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTA-TTG
131 TTAGGGAGATAAGATCTGTAATCCTCAATATATTCCACTGCTGCCCAGGGAG-TAGAATTACTTG
* ** *
3446418 GCTTCAATGTACTCCACTGTAATCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTAC
195 GCTTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTAC
*
3446483 TGCTTAGGGAGACAAGATCTGTAATCTT
260 TACTTAGGGAGACAAGATCTGTAATCTT
3446511 CAATTTGTTC
Statistics
Matches: 260, Mismatches: 26, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
308 253 0.97
309 7 0.03
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (308 bp):
AGGGAGATAAGATCTGTAATCCTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTAATGGCT
TCAATATACTCCACTACAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTAC
TTAGGGAGATAAGATCTGTAATCCTCAATATATTCCACTGCTGCCCAGGGAGTAGAATTACTTGG
CTTCAATATACTCCACTACAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACT
ACTTAGGGAGACAAGATCTGTAATCTTTAATCTATTCCACTGCTGCCC
Found at i:3446588 original size:50 final size:50
Alignment explanation
Indices: 3446534--3446878 Score: 178
Period size: 50 Copynumber: 6.9 Consensus size: 50
3446524 TGTAATGTCG
** * *
3446534 GGGAAACCAGATCCATCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCATCA
*** * * * * ** * *
3446584 GGGAAGTAAGATCCGCCGTTGTGGCTTTAATCTTTTTAATTGCTA-TATCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGC-ACCATCA
3446634 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCA-C-TGCTA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCAT-C-A
* *** * * * * * * ** * **
3446684 AGGAAGTAAGATCTGCTGTTGTGGCTTCAATTTTTTTAAGTGCAATATCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCATCA
3446734 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCA-C-TGCTA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCAT-C-A
* *** * * * * * * ** * **
3446784 AGGAAGTAAGATCTGCTGTTGTGGCTTCAATTTTTTTAAGTGCAATATCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCATCA
* * *
3446834 GGGAAACCAGATCCGCTGTCGTAGCTTTAATCTGTTCCGCTGCAC
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCAC
3446879 TGCTAAGGAA
Statistics
Matches: 203, Mismatches: 83, Indels: 18
0.67 0.27 0.06
Matches are distributed among these distances:
48 2 0.01
49 3 0.01
50 193 0.95
51 3 0.01
52 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.30
Consensus pattern (50 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCATCA
Found at i:3446654 original size:100 final size:100
Alignment explanation
Indices: 3446534--3446923 Score: 611
Period size: 100 Copynumber: 3.9 Consensus size: 100
3446524 TGTAATGTCG
** * * *
3446534 GGGAAACCAGATCCATCGTCGTAGCTTCAATCTGTTCCACCGCACCG-TCAGGGAAGTAAGATCC
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCT-AAGGAAGTAAGATCC
* * *
3446598 GCCGTTGTGGCTTTAATCTTTTTAATTGCTATATCA
65 GCCGTTGTGGCTTCAATCTTTTTAAGTGCAATATCA
*
3446634 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCTG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCG
* *
3446699 CTGTTGTGGCTTCAATTTTTTTAAGTGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAAGTGCAATATCA
*
3446734 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCTG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCG
* *
3446799 CTGTTGTGGCTTCAATTTTTTTAAGTGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAAGTGCAATATCA
* * *
3446834 GGGAAACCAGATCCGCTGTCGTAGCTTTAATCTGTTCCGCTGCACTGCTAAGGAAGTAAGATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCG
3446899 CCGTTGTGGCTTCAATCTTTTTAAG
66 CCGTTGTGGCTTCAATCTTTTTAAG
3446924 GGTGCTAATC
Statistics
Matches: 272, Mismatches: 17, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
100 271 1.00
101 1 0.00
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (100 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCG
CCGTTGTGGCTTCAATCTTTTTAAGTGCAATATCA
Found at i:3447542 original size:65 final size:65
Alignment explanation
Indices: 3447461--3447591 Score: 226
Period size: 65 Copynumber: 2.0 Consensus size: 65
3447451 TTGATGACTC
*
3447461 GTCTAGCGTAGAAAATCCACTACTCAATCATGATGATAATGGGGTAGACGTGAGAGCAGGAAGGG
1 GTCTAGCGTAGAAAATCCAATACTCAATCATGATGATAATGGGGTAGACGTGAGAGCAGGAAGGG
** *
3447526 GTCTAGCGTAGAAAATCCAATACTCGGTCATGATGATAATGGTGTAGACGTGAGAGCAGGAAGGG
1 GTCTAGCGTAGAAAATCCAATACTCAATCATGATGATAATGGGGTAGACGTGAGAGCAGGAAGGG
3447591 G
1 G
3447592 ATTAGTTATT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.33, C:0.15, G:0.32, T:0.21
Consensus pattern (65 bp):
GTCTAGCGTAGAAAATCCAATACTCAATCATGATGATAATGGGGTAGACGTGAGAGCAGGAAGGG
Found at i:3448786 original size:12 final size:11
Alignment explanation
Indices: 3448763--3448795 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
3448753 CCCTATGCGC
3448763 TCAAAA-AAAA
1 TCAAAACAAAA
3448773 TCAAAATCAAAA
1 TCAAAA-CAAAA
3448785 TCAAAACAAAA
1 TCAAAACAAAA
3448796 AGAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 6 0.29
11 5 0.24
12 10 0.48
ACGTcount: A:0.73, C:0.15, G:0.00, T:0.12
Consensus pattern (11 bp):
TCAAAACAAAA
Found at i:3448829 original size:46 final size:46
Alignment explanation
Indices: 3448768--3448857 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
3448758 TGCGCTCAAA
3448768 AAAAATCAAAATCAAAATCAAAACAAAAAGAAGA-AAAAGAAAAATC
1 AAAAATCAAAATCAAAATCAAAACAAAAA-AAGAGAAAAGAAAAATC
** * **
3448814 AAAAATCAAGGTCAAAATGAAAATGAAAAAAGAGAAAAGAAAAA
1 AAAAATCAAAATCAAAATCAAAACAAAAAAAGAGAAAAGAAAAA
3448858 AGAAAATGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
45 4 0.11
46 34 0.89
ACGTcount: A:0.72, C:0.08, G:0.11, T:0.09
Consensus pattern (46 bp):
AAAAATCAAAATCAAAATCAAAACAAAAAAAGAGAAAAGAAAAATC
Found at i:3448855 original size:14 final size:15
Alignment explanation
Indices: 3448832--3448860 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3448822 AGGTCAAAAT
3448832 GAAAATGAAAAAAGA
1 GAAAATGAAAAAAGA
3448847 GAAAA-GAAAAAAGA
1 GAAAATGAAAAAAGA
3448861 AAATGAGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (15 bp):
GAAAATGAAAAAAGA
Found at i:3448872 original size:46 final size:45
Alignment explanation
Indices: 3448768--3448874 Score: 110
Period size: 46 Copynumber: 2.3 Consensus size: 45
3448758 TGCGCTCAAA
**
3448768 AAAAATCAAAATCAAAATCAAAACAAAAAGAAGAAAAAGAAAAATC
1 AAAAATCAAGGTCAAAATCAAAACAAAAAGAAGAAAAAGAAAAA-C
* **
3448814 AAAAATCAAGGTCAAAATGAAAATGAAAA-AAGAGAAAAGAAAAA-
1 AAAAATCAAGGTCAAAATCAAAACAAAAAGAAGA-AAAAGAAAAAC
*
3448858 AGAAAATGAGAGGTCAA
1 A-AAAATCA-AGGTCAA
3448875 GGCGAAAATC
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 10 0.19
46 41 0.79
ACGTcount: A:0.69, C:0.07, G:0.14, T:0.09
Consensus pattern (45 bp):
AAAAATCAAGGTCAAAATCAAAACAAAAAGAAGAAAAAGAAAAAC
Found at i:3449697 original size:16 final size:15
Alignment explanation
Indices: 3449676--3449715 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
3449666 CTTTGAGTCA
3449676 AAAAAATGGAAAAATG
1 AAAAAATGGAAAAA-G
3449692 AAAAAAT-GAAAAAG
1 AAAAAATGGAAAAAG
*
3449706 TAAAAATGGA
1 AAAAAATGGA
3449716 GAGGCTAAGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 7 0.32
15 8 0.36
16 7 0.32
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.12
Consensus pattern (15 bp):
AAAAAATGGAAAAAG
Found at i:3451051 original size:88 final size:88
Alignment explanation
Indices: 3450926--3451187 Score: 400
Period size: 88 Copynumber: 3.0 Consensus size: 88
3450916 GATAAAAAAT
* * * * *
3450926 AAACCTTACCTCTCTCGGTTGTAGTGGAG-TAGGTTGAAGATAGCAGATATTGCCTTCCTGCATT
1 AAACCTTGCCTCCCTCGGTTGTAGTGGAGCT-GGTTGAAGATAGCAGATCTTGCCTTCCTACATC
*
3450990 GACAGCGAAGCAGATCGAAGACAC
65 GACAGTGAAGCAGATCGAAGACAC
*
3451014 AAACCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCGTGCCTTCCTACATCG
1 AAACCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACATCG
3451079 ACAGTGAAGCAGATCGAAGACAC
66 ACAGTGAAGCAGATCGAAGACAC
* * * *
3451102 AAACCTTGCCTCCCTCGGTTGTAATGGAGCTGGTTGAGGATAGTAAATCTTGCCTTCCTACATCG
1 AAACCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACATCG
*
3451167 AAAGTGAAGCAGATCGAAGAC
66 ACAGTGAAGCAGATCGAAGAC
3451188 GGTGAATCTT
Statistics
Matches: 160, Mismatches: 13, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
88 159 0.99
89 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.25, T:0.24
Consensus pattern (88 bp):
AAACCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTACATCG
ACAGTGAAGCAGATCGAAGACAC
Found at i:3451605 original size:44 final size:44
Alignment explanation
Indices: 3451538--3451686 Score: 219
Period size: 44 Copynumber: 3.4 Consensus size: 44
3451528 GAAGAATTTC
* *
3451538 AAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAG
* *
3451582 AAATCTTATTTCTCTGAGATTACAGCGGAGCAGATTGAAGCCAG
1 AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAG
*
3451626 AAATCTTATC-CCCTTGAGATTACAGCGAAGCAGATTGAAGCCAG
1 AAATCTTATCTCCC-TGAGATTACAGCGGAGCAGATTGAAGCCAG
* *
3451670 TAATCCTATCTCCCTGA
1 AAATCTTATCTCCCTGA
3451687 AGTTGCAGTG
Statistics
Matches: 94, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
43 2 0.02
44 89 0.95
45 3 0.03
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (44 bp):
AAATCTTATCTCCCTGAGATTACAGCGGAGCAGATTGAAGCCAG
Found at i:3451700 original size:88 final size:88
Alignment explanation
Indices: 3451537--3451725 Score: 220
Period size: 88 Copynumber: 2.1 Consensus size: 88
3451527 CGAAGAATTT
* * * * * *
3451537 CAAATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAAATCTTATTTCTCTGAGAT
1 CAAATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGAT
* *
3451602 TACAGCGGAGCAGATTGAAGCCA
66 TACAGCGGAGCAGATTAAAACCA
* *
3451625 GAAATCTTATC-CCCTTGAGATTACAGCGAAGCAGATTGAAGCCAGTAATCCTATCTCCCTGA-A
1 CAAATCTTATCTCCC-TGAGATTACAGCGAAGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGA
* * *
3451688 GTTGCAGTGGAGCGGATTAAAACCA
65 -TTACAGCGGAGCAGATTAAAACCA
*
3451713 CAGATCTTATCTC
1 CAAATCTTATCTC
3451726 TCTAAGCAGT
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
87 4 0.05
88 78 0.94
89 1 0.01
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (88 bp):
CAAATCTTATCTCCCTGAGATTACAGCGAAGCAGATTGAAGCCAGAAATCCTATCTCCCTGAGAT
TACAGCGGAGCAGATTAAAACCA
Found at i:3451761 original size:40 final size:40
Alignment explanation
Indices: 3451717--3452032 Score: 170
Period size: 40 Copynumber: 7.5 Consensus size: 40
3451707 AAACCACAGA
* * *
3451717 TCTTATCTCTCTAAGCAGTAGTGGAGCAGATCGCATCAAG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAATCAAG
*
3451757 TCTTATCTCCCTAAGCAGTAGTAGACAAGACAGA-AGAAATCAA-
1 TCTTATCTCCCTAAGCAGTAGT-G--GAG-CAGATAG-AATCAAG
* * ** * * * *
3451800 TCCTATCTCCCTGATGTTGCAGTGGAGCGGATTAAAACCACAG
1 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGA-TAGAATCA-AG
* * * * *
3451843 ATCTTGTCTCCCTAAGCAATAGTGGAGCAAATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAATCAAG
* *
3451884 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAAT-AAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAG--A-TAG-AATCAAG
* * ** * * *
3451927 TCCTATCTCCCTGATGTTGCAGTGGAGCAGATTAAAACCACAG
1 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGA-TAGAATCA-AG
* * * * *
3451970 ATTTTATCTCCCTAAGCAGTAGTGGAGCAGATCGCACCAGG
1 -TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAATCAAG
*
3452011 TCTTATCTCTCTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGT
3452033 CCAGTAGGCT
Statistics
Matches: 202, Mismatches: 55, Indels: 38
0.68 0.19 0.13
Matches are distributed among these distances:
40 70 0.35
41 12 0.06
42 15 0.07
43 55 0.27
44 50 0.25
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (40 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATAGAATCAAG
Found at i:3451780 original size:43 final size:43
Alignment explanation
Indices: 3451717--3452032 Score: 112
Period size: 43 Copynumber: 7.5 Consensus size: 43
3451707 AAACCACAGA
* * *
3451717 TCTTATCTCTCTAAGC---AGTAGTGGAGCAGATCGCATCAAG
1 TCTTATCTCCCTAAGCAGTAGTAGTGGAGCAGATAGAATCAAG
***
3451757 TCTTATCTCCCTAAGCAGTAGTAGACAAGACAGA-AGAAATCAA-
1 TCTTATCTCCCTAAGCAGTAGTAGTGGAG-CAGATAG-AATCAAG
* * * * * *
3451800 TCCTATCTCCCT--G-ATGTTGCAGTGGAGCGGATTAAAACCACAG
1 TCTTATCTCCCTAAGCA-GTAGTAGTGGAGCAGA-TAGAATCA-AG
* * * *
3451843 ATCTTGTCTCCCTAAGCA--A-TAGTGGAGCAAATCGCATCAAG
1 -TCTTATCTCCCTAAGCAGTAGTAGTGGAGCAGATAGAATCAAG
* * * *
3451884 TCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGA-AGAAAT-AAA
1 TCTTATCTCCCTAAGCAGTAGTAGTGGAG-CAGATAG-AATCAAG
* * * * *
3451927 TCCTATCTCCCT--G-ATGTTGCAGTGGAGCAGATTAAAACCACAG
1 TCTTATCTCCCTAAGCA-GTAGTAGTGGAGCAGA-TAGAATCA-AG
* * * * *
3451970 ATTTTATCTCCCTAAGC---AGTAGTGGAGCAGATCGCACCAGG
1 -TCTTATCTCCCTAAGCAGTAGTAGTGGAGCAGATAGAATCAAG
*
3452011 TCTTATCTCTCTAAGCAGTAGT
1 TCTTATCTCCCTAAGCAGTAGT
3452033 CCAGTAGGCT
Statistics
Matches: 193, Mismatches: 52, Indels: 59
0.63 0.17 0.19
Matches are distributed among these distances:
40 54 0.28
41 25 0.13
42 14 0.07
43 63 0.33
44 34 0.18
46 2 0.01
47 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (43 bp):
TCTTATCTCCCTAAGCAGTAGTAGTGGAGCAGATAGAATCAAG
Found at i:3451819 original size:127 final size:127
Alignment explanation
Indices: 3451671--3452032 Score: 600
Period size: 127 Copynumber: 2.9 Consensus size: 127
3451661 TGAAGCCAGT
* *
3451671 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAGCAGT
1 AATCCTATCTCCCTGATGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAAGCAGT
*
3451736 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTAGA-CAAGACAGAAGAAATC
66 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTAGAGC-AGACAGAAGAAATA
* *
3451798 AATCCTATCTCCCTGATGTTGCAGTGGAGCGGATTAAAACCACAGATCTTGTCTCCCTAAGCAAT
1 AATCCTATCTCCCTGATGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAAGCAGT
* *
3451863 AGTGGAGCAAATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAATA
66 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTAGAGCAGACAGAAGAAATA
* *
3451925 AATCCTATCTCCCTGATGTTGCAGTGGAGCAGATTAAAACCACAGATTTTATCTCCCTAAGCAGT
1 AATCCTATCTCCCTGATGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAAGCAGT
* * *
3451990 AGTGGAGCAGATCGCACCAGGTCTTATCTCTCTAAGCAGTAGT
66 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGT
3452033 CCAGTAGGCT
Statistics
Matches: 219, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
127 218 1.00
128 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.21, T:0.25
Consensus pattern (127 bp):
AATCCTATCTCCCTGATGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTAGAGCAGACAGAAGAAATA
Found at i:3452059 original size:127 final size:127
Alignment explanation
Indices: 3451671--3452091 Score: 592
Period size: 127 Copynumber: 3.3 Consensus size: 127
3451661 TGAAGCCAGT
* *
3451671 AATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTAAGCAGT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCCCTAAGCAGT
* *
3451736 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTAGACAAGACAGAAGAAATC
66 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTAGAGAAGACAGAAGAAATA
* * * *
3451798 AATCCTATCTCCCTGATGTTGCAGTGGAGCGGATTAAAACCACAGATCTTGTCTCCCTAAGCAAT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCCCTAAGCAGT
* * *
3451863 AGTGGAGCAAATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTGGAGCAGACAGAAGAAATA
66 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTAGAGAAGACAGAAGAAATA
* *
3451925 AATCCTATCTCCCTGATGTTGCAGTGGAGCAGATTAAAACCACAGATTTTATCTCCCTAAGCAGT
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCCCTAAGCAGT
* * * ** * * * *
3451990 AGTGGAGCAGATCGCACCAGGTCTTATCTCTCTAAGCAGTAGTCCAGTAGGCTGAAGCTAAT-
66 AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTAGAGAAGACAGAAG-AAATA
* * * *
3452052 AACCCTATCTCCCTGAAGTTGTAGTGTAGCAAATTAAAAC
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAC
3452092 GATGAATCTT
Statistics
Matches: 265, Mismatches: 28, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
127 262 0.99
128 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (127 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCACAGATCTTATCTCCCTAAGCAGT
AGTGGAGCAGATCGCATCAAGTCTTATCTCCCTAAGCAGTAGTAGAGAAGACAGAAGAAATA
Found at i:3452581 original size:16 final size:17
Alignment explanation
Indices: 3452551--3452591 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
3452541 GGGCCCAGGG
*
3452551 AAACAGAAA-CAAATCC
1 AAACACAAATCAAATCC
3452567 AAA-ACAAATCAAATCC
1 AAACACAAATCAAATCC
3452583 AAACACAAA
1 AAACACAAA
3452592 ATAAATCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.66, C:0.24, G:0.02, T:0.07
Consensus pattern (17 bp):
AAACACAAATCAAATCC
Found at i:3452982 original size:13 final size:13
Alignment explanation
Indices: 3452962--3452994 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
3452952 TCGATTCTTT
3452962 TTTA-TTTTTAT-
1 TTTATTTTTTATA
3452973 TTTATTTTTTATA
1 TTTATTTTTTATA
3452986 TTTATTTTT
1 TTTATTTTT
3452995 ACTAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 4 0.20
12 7 0.35
13 9 0.45
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTATTTTTTATA
Found at i:3452982 original size:18 final size:18
Alignment explanation
Indices: 3452959--3452993 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3452949 TATTCGATTC
*
3452959 TTTTTTATTTTTATTTTA
1 TTTTTTATATTTATTTTA
3452977 TTTTTTATATTTATTTT
1 TTTTTTATATTTATTTT
3452994 TACTAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTTTATATTTATTTTA
Found at i:3471664 original size:21 final size:21
Alignment explanation
Indices: 3471640--3471703 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
3471630 ACTAACCACA
*
3471640 AACCCCTAACCTCTAACCCTT
1 AACCACTAACCTCTAACCCTT
* * *
3471661 AACCACAAACCTTTAACCCCT
1 AACCACTAACCTCTAACCCTT
* * *
3471682 AACTACTAACCCCTAAACCTT
1 AACCACTAACCTCTAACCCTT
3471703 A
1 A
3471704 TTTAATATAA
Statistics
Matches: 33, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.36, C:0.42, G:0.00, T:0.22
Consensus pattern (21 bp):
AACCACTAACCTCTAACCCTT
Found at i:3471676 original size:14 final size:14
Alignment explanation
Indices: 3471632--3471678 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3471622 CTTAAATCAC
*
3471632 TAACCACAAACCCC
1 TAACCACAAACCCT
* *
3471646 TAACCTCTAACCCT
1 TAACCACAAACCCT
*
3471660 TAACCACAAACCTT
1 TAACCACAAACCCT
3471674 TAACC
1 TAACC
3471679 CCTAACTACT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.38, C:0.43, G:0.00, T:0.19
Consensus pattern (14 bp):
TAACCACAAACCCT
Found at i:3472327 original size:41 final size:41
Alignment explanation
Indices: 3472265--3472540 Score: 365
Period size: 41 Copynumber: 6.7 Consensus size: 41
3472255 AAATGTTTTT
** *
3472265 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCCAAGAGCATTA
1 GCGGCGCTTTACCAAAAACGCCGCTAAAGCCCAGAGCATTA
* * *
3472306 GCGGTGCTTTACTAAAAACGCCGCTAAAGCCTAGAGCATTA
1 GCGGCGCTTTACCAAAAACGCCGCTAAAGCCCAGAGCATTA
* * *
3472347 GTGGCGCTTTCCCAAAAATGCCGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTTACCAAAAACGCCGCTAAAGCCCAGAGCATTA
* *
3472388 GCGGCACTTTACAAAAAACGCCGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTTACCAAAAACGCCGCTAAAGCCCAGAGCATTA
* * *
3472429 GCGGCGCTTTTA-CAAAAATGTCGCTAAATCCCAGAGCATTA
1 GCGGCGC-TTTACCAAAAACGCCGCTAAAGCCCAGAGCATTA
* * *
3472470 GCGGCGCTTTTCGAAAAACGCTGCTAAAGCCCAGAGCATTA
1 GCGGCGCTTTACCAAAAACGCCGCTAAAGCCCAGAGCATTA
* *
3472511 GCGGCGCTTTTCCAAAAACACCGCTAAAGC
1 GCGGCGCTTTACCAAAAACGCCGCTAAAGC
3472541 GCCGAATGGT
Statistics
Matches: 203, Mismatches: 30, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
40 3 0.01
41 196 0.97
42 4 0.02
ACGTcount: A:0.32, C:0.28, G:0.21, T:0.20
Consensus pattern (41 bp):
GCGGCGCTTTACCAAAAACGCCGCTAAAGCCCAGAGCATTA
Found at i:3472627 original size:40 final size:40
Alignment explanation
Indices: 3472577--3472665 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 40
3472567 TGGGCATAGG
* *
3472577 TTTTT-GCGGTGTTTTCTCAAAAAACGCCGCTAATTC-TCA
1 TTTTTAGCGGTGCTTTC-CAAAAAACGCCGCTAATGCTTCA
** * *
3472616 TTTTTAGCGGTGCTTTCCCTAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGTGCTTTCCAAAAAACGCCGCTAATGCTTCA
3472656 TTTTTAGCGG
1 TTTTTAGCGG
3472666 CGTATTTTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
39 20 0.48
40 22 0.52
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGTGCTTTCCAAAAAACGCCGCTAATGCTTCA
Found at i:3472754 original size:2 final size:2
Alignment explanation
Indices: 3472747--3472775 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
3472737 ATGTTCAAAG
3472747 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3472776 GTGATTATTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3475222 original size:11 final size:11
Alignment explanation
Indices: 3475206--3475230 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3475196 AATTCCCAGA
3475206 TTTCTTTTCTT
1 TTTCTTTTCTT
3475217 TTTCTTTTCTT
1 TTTCTTTTCTT
3475228 TTT
1 TTT
3475231 TTTGTATGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:3482266 original size:90 final size:90
Alignment explanation
Indices: 3482161--3482334 Score: 294
Period size: 90 Copynumber: 1.9 Consensus size: 90
3482151 CTCACCCCTA
* *
3482161 GTTTAGGATTTAAGGTATCATTTTTATATTTTCGTGTATTAATTTTTTAGAATGTTTGTATTTTT
1 GTTTAGGATTTAAGGTATCATTTTTATATTTTCATGTATTAATTTCTTAGAATGTTTGTATTTTT
3482226 TTATATCTGTAAATTTAATATAGTT
66 TTATATCTGTAAATTTAATATAGTT
* * *
3482251 GTTTGGGATTTAAGGTTTCATTTTTATATTTTCATGTATTAATTTCTTAGCATGTTTGTATTTTT
1 GTTTAGGATTTAAGGTATCATTTTTATATTTTCATGTATTAATTTCTTAGAATGTTTGTATTTTT
*
3482316 TTGTATCTGTAAATTTAAT
66 TTATATCTGTAAATTTAAT
3482335 TTAATTCGTA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.57
Consensus pattern (90 bp):
GTTTAGGATTTAAGGTATCATTTTTATATTTTCATGTATTAATTTCTTAGAATGTTTGTATTTTT
TTATATCTGTAAATTTAATATAGTT
Found at i:3482397 original size:90 final size:88
Alignment explanation
Indices: 3482188--3482427 Score: 207
Period size: 90 Copynumber: 2.7 Consensus size: 88
3482178 TCATTTTTAT
* * * *
3482188 ATTTTCGTGTATTAATTTTTTAGAATGTTTGTATTTTTTTATATCTGTAAATTTAATATAGTTGT
1 ATTTTCGTGTATTAATTTTTT--CATGTTTGTATTTTTTTGTATCTGTAAATTTAATTTAATTGT
* * * * *
3482253 TTGGGATTTAAGGTTTCATTTTTAT
64 TTGAGATGTAAGGTTTCAATTTAAA
* *
3482278 ATTTTCATGTATTAATTTCTTAGCATGTTTGTATTTTTTTGTATCTGTAAATTTAATTTAATTCG
1 ATTTTCGTGTATTAATTT-TT-TCATGTTTGTATTTTTTTGTATCTGTAAATTTAATTTAATT-G
* *
3482343 TATT-ATATGT-A-GTTTGAATTTAAA
63 T-TTGAGATGTAAGGTTTCAATTTAAA
* * ** * *
3482367 ATTTTCGTGTATTAATTTTTCTCATTTGTTTGTAGTTTGTTGGGTGTTTAAATTTAATTTA
1 ATTTTCGTGTATTAATTTTT-TCA--TGTTTGTATTTTTTTGTATCTGTAAATTTAATTTA
3482428 GTGTGTATTG
Statistics
Matches: 122, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
88 4 0.03
89 26 0.21
90 83 0.68
91 7 0.06
92 2 0.02
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.57
Consensus pattern (88 bp):
ATTTTCGTGTATTAATTTTTTCATGTTTGTATTTTTTTGTATCTGTAAATTTAATTTAATTGTTT
GAGATGTAAGGTTTCAATTTAAA
Found at i:3485164 original size:5 final size:5
Alignment explanation
Indices: 3485135--3485198 Score: 51
Period size: 5 Copynumber: 12.4 Consensus size: 5
3485125 TCATTTAAAC
* * *
3485135 TTTCA TTCCA TTTCA TAATCA --TCA TTTCA TTTTA TATTCA TTTAACA
1 TTTCA TTTCA TTTCA T-TTCA TTTCA TTTCA TTTCA T-TTCA TTT--CA
3485182 TTTCA TTTCA TTTCA TT
1 TTTCA TTTCA TTTCA TT
3485199 ATTTTTTTTC
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
3 3 0.06
5 33 0.69
6 7 0.15
7 5 0.10
ACGTcount: A:0.27, C:0.19, G:0.00, T:0.55
Consensus pattern (5 bp):
TTTCA
Found at i:3485226 original size:23 final size:23
Alignment explanation
Indices: 3485182--3485226 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3485172 TCATTTAACA
*
3485182 TTTCATTTCATTTCATTATTTTT
1 TTTCATTTAATTTCATTATTTTT
3485205 TTTCATTTAAATTT-ATT-TTTTT
1 TTTCATTT-AATTTCATTATTTTT
3485227 CCTAATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.71
Consensus pattern (23 bp):
TTTCATTTAATTTCATTATTTTT
Found at i:3485466 original size:14 final size:14
Alignment explanation
Indices: 3485444--3485477 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3485434 TATCATTTCA
* *
3485444 TTTTCTTTTTGGGT
1 TTTTTTTTTTGAGT
3485458 TTTTTTTTTTGAGT
1 TTTTTTTTTTGAGT
3485472 TTTTTT
1 TTTTTT
3485478 AGGCCTGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.03, C:0.03, G:0.15, T:0.79
Consensus pattern (14 bp):
TTTTTTTTTTGAGT
Found at i:3485673 original size:21 final size:21
Alignment explanation
Indices: 3485648--3485687 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3485638 TTACGTTTGT
*
3485648 TTTGAATTTCTATTTCATTTA
1 TTTGAATTTCCATTTCATTTA
3485669 TTTGAATTTCCATTTCATT
1 TTTGAATTTCCATTTCATT
3485688 CCATTCCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (21 bp):
TTTGAATTTCCATTTCATTTA
Found at i:3485739 original size:21 final size:21
Alignment explanation
Indices: 3485714--3486047 Score: 116
Period size: 21 Copynumber: 14.4 Consensus size: 21
3485704 TTTATTTCTA
*
3485714 TTTCATTTAAATTATATATTT
1 TTTCATTTAAATTATATTTTT
*
3485735 TTTCATTTAAATTTAATTTTTTCT
1 TTTCATTTAAA-TT-ATATTTT-T
*
3485759 CATTTCATTTAAATTATCTTTTT
1 --TTTCATTTAAATTATATTTTT
* *
3485782 TTACATTTAAAATTAATTTTTTTCT
1 TTTCATTT-AAATT-A-TATTTT-T
* *
3485807 CATTTCATTTAAATTATCTTTGT
1 --TTTCATTTAAATTATATTTTT
* *
3485830 TTACATTTTAATTTAATATTTTTCT
1 TTTCA-TTTAAATT-ATA-TTTT-T
* * *
3485855 CATTTCATTTAAATTATCTATCT
1 --TTTCATTTAAATTATATTTTT
** **
3485878 TCCCATTTTCATT-TATTTATT
1 TTTCATTTAAATTATATTT-TT
* *
3485899 TCTCTCATTTCATTTATATTATTT
1 T-T-TCATTTAAATTATATT-TTT
* *
3485923 TTTCCATGTAAATTTAATTTTTTCT
1 TTT-CATTTAAA-TT-ATATTTT-T
*
3485948 TACTTCATTTAAATTATCTTTTT
1 T--TTCATTTAAATTATATTTTT
3485971 TTTCATTTAAATT-TAATTTCTTCCT
1 TTTCATTTAAATTAT-A-TT-TT--T
*
3485996 CATTTCATTTAAATTATATTTCT
1 --TTTCATTTAAATTATATTTTT
*
3486019 TTCCATTTAAATT-TAATTTTT
1 TTTCATTTAAATTAT-ATTTTT
*
3486040 TCTCATTT
1 TTTCATTT
3486048 CATTTAAATT
Statistics
Matches: 235, Mismatches: 41, Indels: 74
0.67 0.12 0.21
Matches are distributed among these distances:
20 5 0.02
21 68 0.29
22 17 0.07
23 29 0.12
24 38 0.16
25 18 0.08
26 32 0.14
27 27 0.11
28 1 0.00
ACGTcount: A:0.26, C:0.13, G:0.01, T:0.60
Consensus pattern (21 bp):
TTTCATTTAAATTATATTTTT
Found at i:3485814 original size:48 final size:48
Alignment explanation
Indices: 3485703--3486057 Score: 422
Period size: 48 Copynumber: 7.5 Consensus size: 48
3485693 CCATTTCCAT
*
3485703 TTTTATTTCT-ATTTCATTTAAATTATATATTTTTT-CATTTAAATTTAA
1 TTTT-TTTCTCATTTCATTTAAATTATCT-TTTTTTCCATTTAAATTTAA
* *
3485751 -TTTTTTCTCATTTCATTTAAATTATCTTTTTTTACATTTAAAATTAA
1 TTTTTTTCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAA
* * *
3485798 TTTTTTTCTCATTTCATTTAAATTATCTTTGTTTACATTTTAATTTAA
1 TTTTTTTCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAA
* * * * **
3485846 TATTTTTCTCATTTCATTTAAATTATCTATCTTCCCATTTTCATTT-A
1 TTTTTTTCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAA
* *
3485893 TTTATTTCTCTCATTTCATTTATATTA---TTTTTTCCATGTAAATTTAA
1 TTT-TTT-TCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAA
* * *
3485940 -TTTTTTCTTACTTCATTTAAATTATCTTTTTTTTCATTTAAATTTAA
1 TTTTTTTCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAA
* * * *
3485987 TTTCTTCCTCATTTCATTTAAATTATATTTCTTTCCATTTAAATTTAA
1 TTTTTTTCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAA
3486035 -TTTTTTCTCATTTCATTTAAATT
1 TTTTTTTCTCATTTCATTTAAATT
3486058 TAATTTTTTT
Statistics
Matches: 264, Mismatches: 33, Indels: 21
0.83 0.10 0.07
Matches are distributed among these distances:
44 16 0.06
45 3 0.01
46 25 0.09
47 75 0.28
48 127 0.48
49 18 0.07
ACGTcount: A:0.26, C:0.12, G:0.01, T:0.61
Consensus pattern (48 bp):
TTTTTTTCTCATTTCATTTAAATTATCTTTTTTTCCATTTAAATTTAA
Found at i:3485937 original size:189 final size:186
Alignment explanation
Indices: 3485716--3486057 Score: 540
Period size: 189 Copynumber: 1.8 Consensus size: 186
3485706 TATTTCTATT
* *
3485716 TCATTTAAATTATATATTTTTTCATTTAAATTTAATTTTTTCTCATTTCATTTAAATTATCTTTT
1 TCATTTAAATTATATATTTTTTCATGTAAATTTAATTTTTTCTCACTTCATTTAAATTATCTTTT
* * * * *
3485781 TTTACATTTAAAATTAATTTTTTTCTCATTTCATTTAAATTATCTTTGTTTACATTTTAATTTAA
66 TTTACATTTAAAATTAATTTCTTCCTCATTTCATTTAAATTATATTTCTTTACATTTAAATTTAA
3485846 TATTTTTCTCATTTCATTTAAATTATCTATCTTCCCATTTTCATTTATTTATTTCTC
131 T-TTTTTCTCATTTCATTTAAATTATCTATCTTCCCATTTTCATTTATTTATTTCTC
* * *
3485903 TCATTTCATTTATATTATTTTTTCCATGTAAATTTAATTTTTTCTTACTTCATTTAAATTATCTT
1 TCATTTAAATTATA-TATTTTTT-CATGTAAATTTAATTTTTTCTCACTTCATTTAAATTATCTT
* * *
3485968 TTTTTTCATTTAAATTTAATTTCTTCCTCATTTCATTTAAATTATATTTCTTTCCATTTAAATTT
64 TTTTTACATTTAAAATTAATTTCTTCCTCATTTCATTTAAATTATATTTCTTTACATTTAAATTT
3486033 AATTTTTTCTCATTTCATTTAAATT
129 AATTTTTTCTCATTTCATTTAAATT
3486058 TAATTTTTTT
Statistics
Matches: 140, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
187 12 0.09
188 30 0.21
189 98 0.70
ACGTcount: A:0.27, C:0.13, G:0.01, T:0.60
Consensus pattern (186 bp):
TCATTTAAATTATATATTTTTTCATGTAAATTTAATTTTTTCTCACTTCATTTAAATTATCTTTT
TTTACATTTAAAATTAATTTCTTCCTCATTTCATTTAAATTATATTTCTTTACATTTAAATTTAA
TTTTTTCTCATTTCATTTAAATTATCTATCTTCCCATTTTCATTTATTTATTTCTC
Found at i:3486095 original size:27 final size:25
Alignment explanation
Indices: 3485734--3486095 Score: 141
Period size: 27 Copynumber: 14.9 Consensus size: 25
3485724 ATTATATATT
*
3485734 TTTTCATTTAAATTTAATTTTTTCTC
1 TTTTCATTTAAA-TTATTTTTTTCTC
* *
3485760 ATTTCATTTAAATTA--TCTTT-T-
1 TTTTCATTTAAATTATTTTTTTCTC
*
3485781 TTTACATTTAAAATTAATTTTTTTCTC
1 TTTTCATTT-AAATT-ATTTTTTTCTC
* *
3485808 ATTTCATTTAAATTATCTTTGTTTAC-A
1 TTTTCATTTAAATTAT-TTT-TTT-CTC
*
3485835 TTTTAATTT-AA-TA--TTTTTCTC
1 TTTTCATTTAAATTATTTTTTTCTC
* * * *
3485856 ATTTCATTTAAATTATCTATCTTCCC
1 TTTTCATTTAAATTAT-TTTTTTCTC
* *
3485882 ATTTTCATTT--ATT-TATTTCTCTC
1 -TTTTCATTTAAATTATTTTTTTCTC
* *
3485905 ATTTCATTTATATTA--TTTTT-TC
1 TTTTCATTTAAATTATTTTTTTCTC
* *
3485927 ----CATGTAAATTTAATTTTTTCT-
1 TTTTCATTTAAA-TTATTTTTTTCTC
* *
3485948 TACTTCATTTAAATTA--TCTTT-T-
1 T-TTTCATTTAAATTATTTTTTTCTC
* *
3485970 TTTTCATTTAAATTTAATTTCTTCCTC
1 TTTTCATTTAAA-TT-ATTTTTTTCTC
* *
3485997 ATTTCATTTAAATTA---TATT-TC
1 TTTTCATTTAAATTATTTTTTTCTC
* *
3486018 TTTCCATTTAAATTTAATTTTTTCTC
1 TTTTCATTTAAA-TTATTTTTTTCTC
*
3486044 ATTTCATTTAAATTTAATTTTTTTCTC
1 TTTTCATTTAAA-TT-ATTTTTTTCTC
3486071 TTTTCATTTAAATTATCTTTCTTTC
1 TTTTCATTTAAATTAT-TTT-TTTC
3486096 CATTTTAATT
Statistics
Matches: 253, Mismatches: 41, Indels: 83
0.67 0.11 0.22
Matches are distributed among these distances:
18 6 0.02
19 3 0.01
20 1 0.00
21 44 0.17
22 29 0.11
23 20 0.08
24 4 0.02
25 27 0.11
26 57 0.23
27 61 0.24
28 1 0.00
ACGTcount: A:0.25, C:0.13, G:0.01, T:0.61
Consensus pattern (25 bp):
TTTTCATTTAAATTATTTTTTTCTC
Found at i:3486116 original size:74 final size:74
Alignment explanation
Indices: 3485713--3486106 Score: 271
Period size: 74 Copynumber: 5.5 Consensus size: 74
3485703 TTTTATTTCT
*
3485713 ATTTCATTTAAATTATATATT-TTTTCATTTAAATTTAATTTTTTCTCATTTCATTTAAA-TT-A
1 ATTTCATTTAAATTATAT-TTCTTTCCATTTAAATTTAATTTTTTCTCATTTCATTTAAATTTAA
3485775 TCTT-TT--T-
65 T-TTCTTCCTC
* * * * * *
3485782 -TTACATTTAAAATTA-ATTTTTTTCTCATTT-CATTTAAATTATCTTTGT--TTACATTTTAAT
1 ATTTCATTT-AAATTATATTTCTTTC-CATTTAAATTT-AATT-T-TTTCTCATTTCATTTAAAT
*
3485842 TTAATATT-TTTCTC
61 TTAAT-TTCTTCCTC
* * * ** * *
3485856 ATTTCATTTAAATTATCTATCTTCCCATTTTCATTTATTTATTTCTCTCATTTCATTTATA-TT-
1 ATTTCATTTAAATTATATTTCTTTCCATTTAAATTTAATT-TTT-TCTCATTTCATTTAAATTTA
*
3485919 ATTT-TTTC-C
64 ATTTCTTCCTC
** * *
3485928 ATGTAAATTT-AATT-T-TTTCTTACTTCATTTAAA-TT-ATCTTTT-T--TTTCATTTAAATTT
1 AT-TTCATTTAAATTATATTTCTT--TCCATTTAAATTTAATTTTTTCTCATTTCATTTAAATTT
3485985 AATTTCTTCCTC
63 AATTTCTTCCTC
3485997 ATTTCATTTAAATTATATTTCTTTCCATTTAAATTTAATTTTTTCTCATTTCATTTAAATTTAAT
1 ATTTCATTTAAATTATATTTCTTTCCATTTAAATTTAATTTTTTCTCATTTCATTTAAATTTAAT
* *
3486062 TTTTTTCTC
66 TTCTTCCTC
* * *
3486071 TTTTCATTTAAATTATCTTTCTTTCCATTTTAATTT
1 ATTTCATTTAAATTATATTTCTTTCCATTTAAATTT
3486107 CCATTTTTCT
Statistics
Matches: 256, Mismatches: 37, Indels: 59
0.73 0.11 0.17
Matches are distributed among these distances:
65 10 0.04
66 2 0.01
67 7 0.03
68 25 0.10
69 43 0.17
70 12 0.05
71 25 0.10
72 14 0.05
73 14 0.05
74 77 0.30
75 19 0.07
76 8 0.03
ACGTcount: A:0.26, C:0.13, G:0.01, T:0.61
Consensus pattern (74 bp):
ATTTCATTTAAATTATATTTCTTTCCATTTAAATTTAATTTTTTCTCATTTCATTTAAATTTAAT
TTCTTCCTC
Found at i:3487185 original size:32 final size:32
Alignment explanation
Indices: 3487144--3487206 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
3487134 CTCCATCGAA
3487144 ATGAACATAAACAAACAAAATTTAGGAACTCC
1 ATGAACATAAACAAACAAAATTTAGGAACTCC
3487176 ATGAACATAAACAAACAAAATTTAGGAACTC
1 ATGAACATAAACAAACAAAATTTAGGAACTC
3487207 ATTTTAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.54, C:0.17, G:0.10, T:0.19
Consensus pattern (32 bp):
ATGAACATAAACAAACAAAATTTAGGAACTCC
Found at i:3489033 original size:34 final size:33
Alignment explanation
Indices: 3488989--3489080 Score: 114
Period size: 34 Copynumber: 2.7 Consensus size: 33
3488979 CTCTTTTTTA
3488989 AAAATTAATTAAATTAGGGTTTAGGGGTTCTAA-
1 AAAATTAATTAAATT-GGGTTTAGGGGTTCTAAG
* * *
3489022 ATAAATTAATTAAAATTGGGTTTAGTGTTTTTAAG
1 A-AAATTAATT-AAATTGGGTTTAGGGGTTCTAAG
3489057 AAAATTAATTAAATTTGGGTTTAG
1 AAAATTAATTAAA-TTGGGTTTAG
3489081 CTTTTTCTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
33 4 0.08
34 42 0.81
35 6 0.12
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.41
Consensus pattern (33 bp):
AAAATTAATTAAATTGGGTTTAGGGGTTCTAAG
Found at i:3489443 original size:126 final size:126
Alignment explanation
Indices: 3489156--3489674 Score: 708
Period size: 125 Copynumber: 4.1 Consensus size: 126
3489146 TTTGGTTTTT
* * *
3489156 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAATACGGTTCTGAACAAATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGGTTTTGAACAAATAGTGTCAAAA
* * * * * **
3489221 ATGCTTCAAGCAGGATGCACTATC-ACCAAATTACTGAAAGAAGCTCCCA-GACAGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAACAAAATTACTGAAAAAAGCTCTCACG-TGGACGCTC
* *
3489281 TTTTTCTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGGTTTTGAACAAATAGTGTCAAAA
* *
3489346 ACGCTTCAAGCAGGATGCACTGTCAACAAAATTGA-TGAAAAAAGCTCTGACGTGGATGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAACAAAATT-ACTGAAAAAAGCTCTCACGTGGACGCTC
* *
3489407 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGTTTTTGAACAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGGTTTTGAACAAATAGTGTCAAAA
** ** * *
3489472 ATACTTCAAATAGGATGCACTGTCAACAAAATCGA-TGAAAAAAGCTCCCA-GTGGACGCTC
66 ACGCTTCAAGCAGGATGCACTGTCAACAAAAT-TACTGAAAAAAGCTCTCACGTGGACGCTC
* * *
3489532 TTTTTCTACAATAGTTCCTGAAAAAATGATTTTGAGAATAC-GTTTCTGAATAAATAGTGTCAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGGTTT-TGAACAAATAGTGTCAAA
** *
3489596 AACGCTTCAAGCAGGATGCACTGTCAGTAAAATTACTGAAAAAAGCTCTCACGTGGATGCTC
65 AACGCTTCAAGCAGGATGCACTGTCAACAAAATTACTGAAAAAAGCTCTCACGTGGACGCTC
3489658 TTTTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
3489675 ATGTTTGGCA
Statistics
Matches: 346, Mismatches: 41, Indels: 13
0.87 0.10 0.03
Matches are distributed among these distances:
124 4 0.01
125 187 0.54
126 153 0.44
127 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (126 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGGTTTTGAACAAATAGTGTCAAAA
ACGCTTCAAGCAGGATGCACTGTCAACAAAATTACTGAAAAAAGCTCTCACGTGGACGCTC
Found at i:3489599 original size:251 final size:251
Alignment explanation
Indices: 3489156--3489674 Score: 776
Period size: 251 Copynumber: 2.1 Consensus size: 251
3489146 TTTGGTTTTT
* *
3489156 TTTTTCTACAGTAGTTCTTGAAAAAATAATTTTGAGAATACGGTTCTGAACAAATAATGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGGTTCTGAACAAATAATGTAAAAA
* * * * *
3489221 ATGCTTCAAGCAGGATGCACTATCACCAAATTACTGAAAGAAGCTCCCAGACAGACGCTCTTTTT
66 ATACTTCAAACAGGATGCACTATCACAAAATGACTGAAAAAAGCTCCCAGACAGACGCTCTTTTT
* *
3489286 CTATAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAAACGCT
131 CTACAATAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAAACGCT
*
3489351 TCAAGCAGGATGCACTGTCAACAAAATTGA-TGAAAAAAGCTCTGACGTGGATGCTC
196 TCAAGCAGGATGCACTGTCAACAAAATT-ACTGAAAAAAGCTCTCACGTGGATGCTC
* * *
3489407 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGTTTTTGAACAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGGTTCTGAACAAATAATGTAAAAA
* * **
3489472 ATACTTCAAATAGGATGCACTGTCAACAAAATCGA-TGAAAAAAGCTCCCAG-TGGACGCTCTTT
66 ATACTTCAAACAGGATGCACTATC-ACAAAAT-GACTGAAAAAAGCTCCCAGACAGACGCTCTTT
* * *
3489535 TTCTACAATAGTTCCTGAAAAAATGATTTTGAGAATAC-GTTTCTGAATAAATAGTGTCAAAAAC
129 TTCTACAATAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTT-TGAACAAATAGTGTCAAAAAC
**
3489599 GCTTCAAGCAGGATGCACTGTCAGTAAAATTACTGAAAAAAGCTCTCACGTGGATGCTC
193 GCTTCAAGCAGGATGCACTGTCAACAAAATTACTGAAAAAAGCTCTCACGTGGATGCTC
3489658 TTTTTCTACAGTAGTTC
1 TTTTTCTACAGTAGTTC
3489675 ATGTTTGGCA
Statistics
Matches: 242, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
250 5 0.02
251 215 0.89
252 21 0.09
253 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (251 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAATACGGTTCTGAACAAATAATGTAAAAA
ATACTTCAAACAGGATGCACTATCACAAAATGACTGAAAAAAGCTCCCAGACAGACGCTCTTTTT
CTACAATAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTTTGAACAAATAGTGTCAAAAACGCT
TCAAGCAGGATGCACTGTCAACAAAATTACTGAAAAAAGCTCTCACGTGGATGCTC
Found at i:3491764 original size:21 final size:21
Alignment explanation
Indices: 3491740--3491855 Score: 106
Period size: 21 Copynumber: 5.5 Consensus size: 21
3491730 ACTCATATGA
3491740 GTTTCAGTTTAACCCTTTTGG
1 GTTTCAGTTTAACCCTTTTGG
* * **
3491761 GTTTCAGTTCAACTCTTTTAA
1 GTTTCAGTTTAACCCTTTTGG
**
3491782 GTTTCAGTTTAACCCTAGTGG
1 GTTTCAGTTTAACCCTTTTGG
* * * * *
3491803 GTTTTAGTTTAGCTCTTCTGA
1 GTTTCAGTTTAACCCTTTTGG
* **
3491824 GCTTCAGTTTAACCCTAATGG
1 GTTTCAGTTTAACCCTTTTGG
3491845 GTTTCAGTTTA
1 GTTTCAGTTTA
3491856 GCTATTCTGA
Statistics
Matches: 71, Mismatches: 24, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 71 1.00
ACGTcount: A:0.19, C:0.18, G:0.18, T:0.45
Consensus pattern (21 bp):
GTTTCAGTTTAACCCTTTTGG
Found at i:3491773 original size:42 final size:42
Alignment explanation
Indices: 3491722--3491933 Score: 162
Period size: 42 Copynumber: 5.1 Consensus size: 42
3491712 TCTCATGAGC
*
3491722 TTCA-TTCAACTCATATGAGTTTCAGTTTAACCCTTTTGGGT
1 TTCAGTTCAACTCATATGAGTTTCAGTTTAACCCTTATGGGT
* * *
3491763 TTCAGTTCAACTCTTTTAAGTTTCAGTTTAACCC-TAGTGGGT
1 TTCAGTTCAACTCATATGAGTTTCAGTTTAACCCTTA-TGGGT
* * * * * * *
3491805 TTTAGTTTAGCTCTTCTGAGCTTCAGTTTAACCCTAATGGGT
1 TTCAGTTCAACTCATATGAGTTTCAGTTTAACCCTTATGGGT
* * * * * * * *
3491847 TTCAGTTTAGCT-ATTCTGAGCTTCAGATTATCTCTTATGGAT
1 TTCAGTTCAACTCA-TATGAGTTTCAGTTTAACCCTTATGGGT
* * * *
3491889 TTCCGTTCAACTCCTATGAGCTTCCA-TTTAACCCTTACGGGT
1 TTCAGTTCAACTCATATGAG-TTTCAGTTTAACCCTTATGGGT
3491931 TTC
1 TTC
3491934 CGTTTAACAC
Statistics
Matches: 135, Mismatches: 30, Indels: 11
0.77 0.17 0.06
Matches are distributed among these distances:
41 5 0.04
42 126 0.93
43 4 0.03
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.42
Consensus pattern (42 bp):
TTCAGTTCAACTCATATGAGTTTCAGTTTAACCCTTATGGGT
Found at i:3491871 original size:21 final size:21
Alignment explanation
Indices: 3491808--3491882 Score: 69
Period size: 21 Copynumber: 3.6 Consensus size: 21
3491798 AGTGGGTTTT
3491808 AGTTTAGCTCTTCTGAGCTTC
1 AGTTTAGCTCTTCTGAGCTTC
* * ** * *
3491829 AGTTTAACCCTAATGGGTTTC
1 AGTTTAGCTCTTCTGAGCTTC
*
3491850 AGTTTAGCTATTCTGAGCTTC
1 AGTTTAGCTCTTCTGAGCTTC
* *
3491871 AGATTATCTCTT
1 AGTTTAGCTCTT
3491883 ATGGATTTCC
Statistics
Matches: 38, Mismatches: 16, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.43
Consensus pattern (21 bp):
AGTTTAGCTCTTCTGAGCTTC
Found at i:3495638 original size:24 final size:25
Alignment explanation
Indices: 3495598--3495645 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
3495588 ACTTCTATTT
*
3495598 TATTAAAAATATAAAAATAATTTAC
1 TATTAAAAATATAAAAAAAATTTAC
*
3495623 TATT-AAAATATTAAAAAAATTTA
1 TATTAAAAATATAAAAAAAATTTA
3495646 TTTTATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (25 bp):
TATTAAAAATATAAAAAAAATTTAC
Found at i:3495656 original size:25 final size:27
Alignment explanation
Indices: 3495593--3495656 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 27
3495583 AAAGGACTTC
*
3495593 TATTTTATTAAAAATATAAAAATAATT
1 TATTTTATTAAATATATAAAAATAATT
*
3495620 TA--CTATTAAA-ATATTAAAAA-AATT
1 TATTTTATTAAATATA-TAAAAATAATT
3495644 TATTTTATTAAAT
1 TATTTTATTAAAT
3495657 GAAACAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
24 9 0.29
25 13 0.42
26 7 0.23
27 2 0.06
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
TATTTTATTAAATATATAAAAATAATT
Found at i:3497138 original size:17 final size:17
Alignment explanation
Indices: 3497113--3497165 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
3497103 TTGTTGAAGA
*
3497113 ATCTATTTGGATTTTGC
1 ATCTGTTTGGATTTTGC
*
3497130 ATCTGTTT-G--TTT-A
1 ATCTGTTTGGATTTTGC
3497143 ATCTGTTTGGATTTTGC
1 ATCTGTTTGGATTTTGC
3497160 ATCTGT
1 ATCTGT
3497166 CTGTTGAAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
13 8 0.28
14 4 0.14
16 4 0.14
17 13 0.45
ACGTcount: A:0.15, C:0.11, G:0.19, T:0.55
Consensus pattern (17 bp):
ATCTGTTTGGATTTTGC
Found at i:3497152 original size:30 final size:30
Alignment explanation
Indices: 3497112--3497170 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3497102 TTTGTTGAAG
*
3497112 AATCTATTTGGATTTTGCATCTGTTTGTTT
1 AATCTATTTGGATTTTGCATCTGTCTGTTT
*
3497142 AATCTGTTTGGATTTTGCATCTGTCTGTT
1 AATCTATTTGGATTTTGCATCTGTCTGTT
3497171 GAAGAATCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.15, C:0.12, G:0.19, T:0.54
Consensus pattern (30 bp):
AATCTATTTGGATTTTGCATCTGTCTGTTT
Found at i:3498796 original size:20 final size:20
Alignment explanation
Indices: 3498771--3498808 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3498761 ACAATTTAAA
*
3498771 ATATAAGTATATTAATATGT
1 ATATAAATATATTAATATGT
*
3498791 ATATAAATTTATTAATAT
1 ATATAAATATATTAATAT
3498809 ATGTAAAAAT
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:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
ATATAAATATATTAATATGT
Found at i:3498818 original size:20 final size:20
Alignment explanation
Indices: 3498780--3498818 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3498770 AATATAAGTA
* *
3498780 TATTAATATGTATATAAATT
1 TATTAATATATATAAAAATT
*
3498800 TATTAATATATGTAAAAAT
1 TATTAATATATATAAAAAT
3498819 AACTTTTTCG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (20 bp):
TATTAATATATATAAAAATT
Found at i:3498930 original size:19 final size:21
Alignment explanation
Indices: 3498895--3498936 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
3498885 CAAACACCAG
3498895 AAAGTAAATCATTTTTC-AGA
1 AAAGTAAATCATTTTTCTAGA
3498915 AAAGTAAATCA-TTTTCTAGA
1 AAAGTAAATCATTTTTCTAGA
3498935 AA
1 AA
3498937 TCATTTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAGTAAATCATTTTTCTAGA
Found at i:3498939 original size:14 final size:14
Alignment explanation
Indices: 3498920--3498971 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
3498910 TCAGAAAAGT
3498920 AAATCATTTTCTAG
1 AAATCATTTTCTAG
3498934 AAATCATTTTCTAG
1 AAATCATTTTCTAG
* *
3498948 AAATTATTTTCCAG
1 AAATCATTTTCTAG
*
3498962 AAAACATTTT
1 AAATCATTTT
3498972 ACTGGCAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.42
Consensus pattern (14 bp):
AAATCATTTTCTAG
Found at i:3499016 original size:7 final size:7
Alignment explanation
Indices: 3499006--3499037 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
3498996 TTATATACAT
3499006 AATACTA
1 AATACTA
3499013 AATACTA
1 AATACTA
3499020 AATACTA
1 AATACTA
3499027 AATACTA
1 AATACTA
3499034 AATA
1 AATA
3499038 TTTTATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:3500209 original size:30 final size:30
Alignment explanation
Indices: 3500175--3500239 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
3500165 ATTAATTAAA
3500175 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
*
3500205 GAGAGCTTTGAGAAATTTAGGGAGAAATTT
1 GAGAGCTTTGAGAAATTTAAGGAGAAATTT
3500235 GAGAG
1 GAGAG
3500240 TTTTTTGCTA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.38, C:0.03, G:0.31, T:0.28
Consensus pattern (30 bp):
GAGAGCTTTGAGAAATTTAAGGAGAAATTT
Found at i:3519308 original size:36 final size:36
Alignment explanation
Indices: 3519268--3519337 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
3519258 AGGGATCTTA
*
3519268 ATGTCGCAACACTCTCAACAATGATACCATCTTGAC
1 ATGTCACAACACTCTCAACAATGATACCATCTTGAC
***
3519304 ATGTCATGGCACTCTCAACAATGATACCATCTTG
1 ATGTCACAACACTCTCAACAATGATACCATCTTG
3519338 GCTTTGGGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (36 bp):
ATGTCACAACACTCTCAACAATGATACCATCTTGAC
Found at i:3521610 original size:37 final size:37
Alignment explanation
Indices: 3521569--3521642 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
3521559 ACTTTTTACT
3521569 TTAACTTATGATTATATAAAGGATATGGTTTAACATA
1 TTAACTTATGATTATATAAAGGATATGGTTTAACATA
3521606 TTAACTTATGATTATATAAAGGATATGGTTTAACATA
1 TTAACTTATGATTATATAAAGGATATGGTTTAACATA
3521643 AGTTTTTCTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.05, G:0.14, T:0.41
Consensus pattern (37 bp):
TTAACTTATGATTATATAAAGGATATGGTTTAACATA
Found at i:3522563 original size:27 final size:27
Alignment explanation
Indices: 3522524--3522576 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
3522514 AATAAACACC
*
3522524 AAAAATTTATTTAAAAAATAAAAAATAA
1 AAAAATATATTT-AAAAATAAAAAATAA
*
3522552 AAAAATAT-TTTAAAATTAAAAAATA
1 AAAAATATATTTAAAAATAAAAAATA
3522577 TTTATTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 13 0.57
27 3 0.13
28 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
AAAAATATATTTAAAAATAAAAAATAA
Found at i:3522572 original size:18 final size:18
Alignment explanation
Indices: 3522545--3522579 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3522535 TAAAAAATAA
3522545 AAAATAAAAAAATATTTT
1 AAAATAAAAAAATATTTT
*
3522563 AAAATTAAAAAATATTT
1 AAAATAAAAAAATATTT
3522580 ATTTATTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATAAAAAAATATTTT
Found at i:3532459 original size:12 final size:12
Alignment explanation
Indices: 3532444--3532477 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
3532434 AAGTCGAACC
3532444 ATAAATATTTTT
1 ATAAATATTTTT
3532456 ATAAATATTTTT
1 ATAAATATTTTT
3532468 ATAAATATTT
1 ATAAATATTT
3532478 ATGGAGTGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATAAATATTTTT
Found at i:3533415 original size:46 final size:46
Alignment explanation
Indices: 3533149--3533413 Score: 431
Period size: 46 Copynumber: 5.8 Consensus size: 46
3533139 TGGAACGTAT
*
3533149 GTATGGTATTTCAGTAAAGAAAACCATATTGAGTTGTGAAAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
*
3533195 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAGAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
* *
3533241 GTATGATATTTCAGTAAAGAAAACCATACTGAGTTGTGAGAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
* *
3533287 GTATGGTATTTTAGTAATGAAAACCATACTGAGTTGTGAAAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
* *
3533333 GTATGGTATTTCAGTAATGAAAACCATACTGAGTTATGAAAAGTAG
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
* * *
3533379 GTATGGTATTTCAGTGAAGAAAATCATATTGAGTT
1 GTATGGTATTTCAGTAAAGAAAACCATACTGAGTT
3533414 ATAGCATTGT
Statistics
Matches: 206, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 206 1.00
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.31
Consensus pattern (46 bp):
GTATGGTATTTCAGTAAAGAAAACCATACTGAGTTGTGAAAAGTAG
Found at i:3546372 original size:20 final size:20
Alignment explanation
Indices: 3546344--3546392 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
3546334 ATATATCCTG
* *
3546344 ATTTTATTTTATTTCAATCA
1 ATTTGATTTGATTTCAATCA
*
3546364 ATTTGATTTGATTTTAATCA
1 ATTTGATTTGATTTCAATCA
*
3546384 AATTGATTT
1 ATTTGATTT
3546393 AATTGCTCCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (20 bp):
ATTTGATTTGATTTCAATCA
Found at i:3547190 original size:11 final size:11
Alignment explanation
Indices: 3547174--3547205 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
3547164 ACCAAAAATT
3547174 TATTTTAAAAA
1 TATTTTAAAAA
3547185 TATTTTAAAAA
1 TATTTTAAAAA
3547196 TATTTTAAAA
1 TATTTTAAAA
3547206 TTAAAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:3547211 original size:17 final size:17
Alignment explanation
Indices: 3547189--3547222 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3547179 TAAAAATATT
* *
3547189 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
3547206 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
3547223 AGTATTTTAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:3547218 original size:29 final size:29
Alignment explanation
Indices: 3547178--3547260 Score: 87
Period size: 28 Copynumber: 2.8 Consensus size: 29
3547168 AAAATTTATT
* *
3547178 TTAAAAATATTTTAAAAA-TATTTTAAAA
1 TTAAAAAAAATTTAAAAAGTATTTTAAAA
**
3547206 TTAAAAAAAATTTAAAAAGTATTTTAATT
1 TTAAAAAAAATTTAAAAAGTATTTTAAAA
3547235 TTAAATTAAAAAATTTAAAAAAGTAT
1 TT-AA--AAAAAATTT-AAAAAGTAT
3547261 GTAAAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 16 0.35
29 10 0.22
30 2 0.04
32 9 0.20
33 9 0.20
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (29 bp):
TTAAAAAAAATTTAAAAAGTATTTTAAAA
Found at i:3547650 original size:28 final size:27
Alignment explanation
Indices: 3547619--3547691 Score: 94
Period size: 28 Copynumber: 2.7 Consensus size: 27
3547609 AATTTTAGGA
3547619 ATTAAATGCATAGAAAAAACATTAAGAC
1 ATTAAATGCA-AGAAAAAACATTAAGAC
**
3547647 ATTAAATGCAAGGAAAAATTATTAAGAC
1 ATTAAATGCAA-GAAAAAACATTAAGAC
*
3547675 ATTAAATG-AAGAGAAAA
1 ATTAAATGCAAGAAAAAA
3547692 TGTTATTGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
26 5 0.12
27 3 0.08
28 32 0.80
ACGTcount: A:0.58, C:0.07, G:0.14, T:0.22
Consensus pattern (27 bp):
ATTAAATGCAAGAAAAAACATTAAGAC
Found at i:3550445 original size:58 final size:57
Alignment explanation
Indices: 3550305--3550447 Score: 180
Period size: 58 Copynumber: 2.5 Consensus size: 57
3550295 ATAAAAATAA
* * *
3550305 ATATTTATATAAATAAATAGATTGAAATATGATTAAATTATATATTATTTTATTAAATT
1 ATATTTA-AT-AATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAATT
* * *
3550364 ATATTTAATAATAATTATGTTAAAATATGGTTAAATTATTTATTATTTTTATTAAATT
1 ATATTTAATAATAATTATATTAAAATATGATTAAATTATATATTA-TTTTATTAAATT
*
3550422 ATTTTTAATAATAATCT-TATTAAAAT
1 ATATTTAATAATAAT-TATATTAAAAT
3550448 TTAATAACAA
Statistics
Matches: 74, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 30 0.41
58 36 0.49
59 8 0.11
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.50
Consensus pattern (57 bp):
ATATTTAATAATAATTATATTAAAATATGATTAAATTATATATTATTTTATTAAATT
Found at i:3550635 original size:16 final size:16
Alignment explanation
Indices: 3550614--3550652 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3550604 TTGATTACTG
*
3550614 ATTACAGCTTTATTCA
1 ATTACAGCTCTATTCA
*
3550630 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCA
3550646 ATTACAG
1 ATTACAG
3550653 TGAAGCAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:3574122 original size:2 final size:2
Alignment explanation
Indices: 3574110--3574140 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3574100 GTGTTTTGCT
*
3574110 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
3574141 GTGCACTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:3577758 original size:87 final size:87
Alignment explanation
Indices: 3577662--3577850 Score: 378
Period size: 87 Copynumber: 2.2 Consensus size: 87
3577652 AATAAATTCC
3577662 TTTTACTTATAAATTTATTCAAAGTATTATAATTATGTTTAAAAAAAATCAGAGATTTCTATAAA
1 TTTTACTTATAAATTTATTCAAAGTATTATAATTATGTTTAAAAAAAATCAGAGATTTCTATAAA
3577727 ATTTATATATTAGGTAATAATA
66 ATTTATATATTAGGTAATAATA
3577749 TTTTACTTATAAATTTATTCAAAGTATTATAATTATGTTTAAAAAAAATCAGAGATTTCTATAAA
1 TTTTACTTATAAATTTATTCAAAGTATTATAATTATGTTTAAAAAAAATCAGAGATTTCTATAAA
3577814 ATTTATATATTAGGTAATAATA
66 ATTTATATATTAGGTAATAATA
3577836 TTTTACTTATAAATT
1 TTTTACTTATAAATT
3577851 AATTTGACTT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
87 102 1.00
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (87 bp):
TTTTACTTATAAATTTATTCAAAGTATTATAATTATGTTTAAAAAAAATCAGAGATTTCTATAAA
ATTTATATATTAGGTAATAATA
Found at i:3602006 original size:132 final size:132
Alignment explanation
Indices: 3601769--3602308 Score: 918
Period size: 132 Copynumber: 4.1 Consensus size: 132
3601759 NNNNNNNNNN
*
3601769 GGGAAGTAGAATTACTAGCTTCAATGTACTCCACTATAACCACGGGGAGGTAAAATCCGCCATCT
1 GGGAAGTAGAATTACTAGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCT
* *
3601834 TCGATCTGCTCCATTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC
66 TCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC
*
3601899 TA
131 CA
* * * *
3601901 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATAT
1 GGGAAGTAGAATTACTAGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCT
* * * * *
3601966 TCAATCTGCTCCACTACTTCTTCGGGAGATAAGATCTGAAATCTTCAATTTATTCCACTATTGCC
66 TCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC
3602031 CA
131 CA
* * *
3602033 TGGAAGTAGAATTACTAGCTTCAATGTACTCCACTGTAACCACAAGGAGGTAAAATCCGCCATCT
1 GGGAAGTAGAATTACTAGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCT
3602098 TCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC
66 TCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC
3602163 CA
131 CA
* *
3602165 GGGAAGTAGAATTACTGGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATTCGCCATCT
1 GGGAAGTAGAATTACTAGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCT
3602230 TCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC
66 TCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC
3602295 CA
131 CA
3602297 GGGAAGTAGAAT
1 GGGAAGTAGAAT
3602309 NNNNNNNNNN
Statistics
Matches: 380, Mismatches: 28, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
132 380 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (132 bp):
GGGAAGTAGAATTACTAGCTTCAATGTACTCCACTATAACCACAGGGAGGTAAAATCCGCCATCT
TCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC
CA
Found at i:3602300 original size:44 final size:45
Alignment explanation
Indices: 3601856--3602300 Score: 126
Period size: 44 Copynumber: 10.1 Consensus size: 45
3601846 ATTACTGCTT
* * *
3601856 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC-T
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGCCAC
* * **
3601900 AGGGA-AGT-AGAATTACTG---GCTTCAATGTACTCCACTGTAACCAC
1 AGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTACTCCACTGTTGCCAC
* * ** * * * **
3601944 AGGGAGGTAAAATCTGCCATATTCAATCTGCTCCACTACTT-CTTC
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACT-GTTGCCAC
* * *
3601989 -GGGAGATAAGATCTGAAATCTTCAATTTATTCCACTATTGCC-C
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGCCAC
* * * * **
3602032 ATGGA-AGT-AGAAT-T-ACTAGCTTCAATGTACTCCACTGTAACCAC
1 AGGGAGA-TAAG-ATCTGA-AATCTTCAATCTACTCCACTGTTGCCAC
* * * * ** * ** **
3602076 AAGGAGGTAAAATCCGCCATCTTCAATCTGCTCCACTACTG-CTT
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGCCAC
* *
3602120 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC-C
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGCCAC
* * * **
3602164 AGGGA-AGT-AGAATTACTG---GCTTCAATGTACTCCACTATAACCAC
1 AGGGAGA-TAAG-A-T-CTGAAATCTTCAATCTACTCCACTGTTGCCAC
* * ** * ** **
3602208 AGGGAGGTAAAAT-TCGCCATCTTCAATCTGCTCCACTACTG-CTT
1 AGGGAGATAAGATCT-GAAATCTTCAATCTACTCCACTGTTGCCAC
* *
3602252 AGGGAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTC-C
1 AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGCCAC
3602296 AGGGA
1 AGGGA
3602301 AGTAGAATNN
Statistics
Matches: 279, Mismatches: 87, Indels: 70
0.64 0.20 0.16
Matches are distributed among these distances:
41 1 0.00
42 5 0.02
43 69 0.25
44 141 0.51
45 56 0.20
46 7 0.03
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (45 bp):
AGGGAGATAAGATCTGAAATCTTCAATCTACTCCACTGTTGCCAC
Found at i:3611458 original size:39 final size:39
Alignment explanation
Indices: 3611402--3611482 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
3611392 AAAATCTTGT
* * *
3611402 TTACATTGATTTTATTCTCAAT-CTTTTATTTCTTTCCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTCCTTT-CCA
3611441 TTACATTGATTTGATTCTCAATCCTTTGATTCCTTTCCA
1 TTACATTGATTTGATTCTCAATCCTTTGATTCCTTTCCA
3611480 TTA
1 TTA
3611483 TTGTTTTGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 27 0.71
40 11 0.29
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (39 bp):
TTACATTGATTTGATTCTCAATCCTTTGATTCCTTTCCA
Found at i:3611842 original size:20 final size:20
Alignment explanation
Indices: 3611817--3611856 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3611807 CTTTGAATAC
3611817 TTATAAATAAATA-TAATTAA
1 TTATAAATAAA-AGTAATTAA
*
3611837 TTATAATTAAAAGTAATTAA
1 TTATAAATAAAAGTAATTAA
3611857 ATTTTTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (20 bp):
TTATAAATAAAAGTAATTAA
Found at i:3619520 original size:18 final size:19
Alignment explanation
Indices: 3619473--3619520 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
3619463 TAAAGTAAAT
*
3619473 ATAAAATTATATCCTTATA
1 ATAATATTATATCCTTATA
3619492 ATAATATTTATAT-CTT-TA
1 ATAATA-TTATATCCTTATA
3619510 ATATATATTAT
1 ATA-ATATTAT
3619521 TTTTGGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 9 0.35
19 11 0.42
20 6 0.23
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAATATTATATCCTTATA
Found at i:3630227 original size:22 final size:22
Alignment explanation
Indices: 3630202--3630243 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
3630192 GCTTTCATGT
*
3630202 TGTTTCGTTGTTGTTTTGCTGC
1 TGTTTCGTTGTTATTTTGCTGC
*
3630224 TGTTTTGTTGTTATTTTGCT
1 TGTTTCGTTGTTATTTTGCT
3630244 ACCATATTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.02, C:0.10, G:0.24, T:0.64
Consensus pattern (22 bp):
TGTTTCGTTGTTATTTTGCTGC
Found at i:3641683 original size:5 final size:5
Alignment explanation
Indices: 3641667--3641695 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
3641657 CTTTCGCATC
3641667 TCTTT T-TTT TCTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
3641696 CTAAATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:3658739 original size:3 final size:3
Alignment explanation
Indices: 3658733--3658782 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
3658723 ATAATAATAA
*
3658733 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG AAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
3658781 TA
1 TA
3658783 ACAGTGGAGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
TAG
Found at i:3666194 original size:26 final size:26
Alignment explanation
Indices: 3666153--3666205 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
3666143 TAAATGAAAG
**
3666153 TGACACTTCGGAGCATTTTAGTGATT
1 TGACACTTCGGAGCATTACAGTGATT
3666179 TGACACTTC-GACGCATTACAGTGATT
1 TGACACTTCGGA-GCATTACAGTGATT
3666205 T
1 T
3666206 TGTACTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (26 bp):
TGACACTTCGGAGCATTACAGTGATT
Found at i:3670265 original size:46 final size:45
Alignment explanation
Indices: 3670212--3670351 Score: 235
Period size: 46 Copynumber: 3.0 Consensus size: 45
3670202 CCATGTAAAA
3670212 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAACTCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAC-CATACTGAG
3670258 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAG-AAACCATACTGAG
* *
3670304 TTGTGAAAAGTAGGTATGGTATTTCCGTGAAGAAAGCCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAA-CCATACTGAG
3670350 TT
1 TT
3670352 ATAGCAATGA
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
45 3 0.03
46 83 0.92
47 4 0.04
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.30
Consensus pattern (45 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAACCATACTGAG
Found at i:3673330 original size:31 final size:32
Alignment explanation
Indices: 3673287--3673346 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
3673277 TAGCGGCACT
*
3673287 TTTCCCACAAACGTCGCTAA-AGAATATGAGGC
1 TTTCCCACAAACGCCG-TAATAGAATATGAGGC
3673319 TTTCCC-CAAACGCCGTAATAGAATATGA
1 TTTCCCACAAACGCCGTAATAGAATATGA
3673347 CATTTAGCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 3 0.12
31 17 0.65
32 6 0.23
ACGTcount: A:0.35, C:0.25, G:0.17, T:0.23
Consensus pattern (32 bp):
TTTCCCACAAACGCCGTAATAGAATATGAGGC
Found at i:3673753 original size:21 final size:21
Alignment explanation
Indices: 3673729--3673775 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3673719 TGCTTTGCTT
*
3673729 TGCTTCCCTCACTGTTGCCTC
1 TGCTTCCCTCACTGCTGCCTC
*
3673750 TGCTTCCCTCGCTGCTGCCTC
1 TGCTTCCCTCACTGCTGCCTC
*
3673771 CGCTT
1 TGCTT
3673776 TAAGTTGTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.02, C:0.45, G:0.17, T:0.36
Consensus pattern (21 bp):
TGCTTCCCTCACTGCTGCCTC
Found at i:3681235 original size:26 final size:26
Alignment explanation
Indices: 3681179--3681239 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
3681169 AAGTATATAT
*
3681179 TTATGTATTACGTAAGTTATGATATG
1 TTATGTATTACGTAAGTTATGATAAG
* * *
3681205 ATATGTATTTATGTGAGTTATG-TAAG
1 TTATGTA-TTACGTAAGTTATGATAAG
3681231 TTATG-ATTA
1 TTATGTATTA
3681240 TCATCTTTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 3 0.10
25 1 0.03
26 13 0.45
27 12 0.41
ACGTcount: A:0.31, C:0.02, G:0.20, T:0.48
Consensus pattern (26 bp):
TTATGTATTACGTAAGTTATGATAAG
Found at i:3682341 original size:2 final size:2
Alignment explanation
Indices: 3682334--3682358 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3682324 AAGCATAAGA
3682334 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 A
3682359 ACCGTCCACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3682546 original size:24 final size:24
Alignment explanation
Indices: 3682514--3682566 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
3682504 AGTATTTTAT
*
3682514 AATACAATATTAATTTTAGATACA
1 AATATAATATTAATTTTAGATACA
**
3682538 AATATAATATTAATTTTTTATACA
1 AATATAATATTAATTTTAGATACA
3682562 AATAT
1 AATAT
3682567 TATACAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (24 bp):
AATATAATATTAATTTTAGATACA
Found at i:3684253 original size:72 final size:73
Alignment explanation
Indices: 3684123--3684282 Score: 225
Period size: 72 Copynumber: 2.2 Consensus size: 73
3684113 GCTCGATCTA
* * *
3684123 TTGCGGCGTTTTTCACCTAGCACCGCTAATGCCACTAAAAACGAAGCCATTTGATTTAAAGTAAA
1 TTGCAGCGTTTTTTACCTAACACCGCTAATGCCACTAAAAACGAAGCCATTTGATTTAAAGTAAA
3684188 ATG-TTTT
66 ATGTTTTT
* * ** *
3684195 TTGCAGCGTTTTTTACCTAACGCCGCTAATGCCACTAAAAATGGCGCCGTTTTG-TTTAAAGTAA
1 TTGCAGCGTTTTTTACCTAACACCGCTAATGCCACTAAAAACGAAGCC-ATTTGATTTAAAGTAA
3684259 AATGTTTTT
65 AATGTTTTT
3684268 TTGCAGCGTTTTTTA
1 TTGCAGCGTTTTTTA
3684283 TTAAAAAGCC
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
72 55 0.71
73 23 0.29
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.36
Consensus pattern (73 bp):
TTGCAGCGTTTTTTACCTAACACCGCTAATGCCACTAAAAACGAAGCCATTTGATTTAAAGTAAA
ATGTTTTT
Found at i:3684437 original size:34 final size:35
Alignment explanation
Indices: 3684390--3684456 Score: 127
Period size: 34 Copynumber: 1.9 Consensus size: 35
3684380 ATTTAATTTG
3684390 TAATATTTTATAATTGTGTACGAAAATAATTTTTA
1 TAATATTTTATAATTGTGTACGAAAATAATTTTTA
3684425 TAATA-TTTATAATTGTGTACGAAAATAATTTT
1 TAATATTTTATAATTGTGTACGAAAATAATTTT
3684457 AAAAAATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 27 0.84
35 5 0.16
ACGTcount: A:0.40, C:0.03, G:0.09, T:0.48
Consensus pattern (35 bp):
TAATATTTTATAATTGTGTACGAAAATAATTTTTA
Found at i:3684796 original size:7 final size:7
Alignment explanation
Indices: 3684778--3684845 Score: 64
Period size: 7 Copynumber: 9.6 Consensus size: 7
3684768 CAAAAAAAAA
*
3684778 CTAAACA
1 CTAAACC
3684785 CTAAACC
1 CTAAACC
*
3684792 ATAAAACC
1 CT-AAACC
3684800 CTAAACC
1 CTAAACC
*
3684807 CTAGACC
1 CTAAACC
*
3684814 TTAAACC
1 CTAAACC
* *
3684821 TTAAATC
1 CTAAACC
*
3684828 TTAAACC
1 CTAAACC
3684835 CTAAACC
1 CTAAACC
3684842 CTAA
1 CTAA
3684846 TATAAAATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
7 45 0.88
8 6 0.12
ACGTcount: A:0.46, C:0.32, G:0.01, T:0.21
Consensus pattern (7 bp):
CTAAACC
Found at i:3684925 original size:40 final size:40
Alignment explanation
Indices: 3684870--3685034 Score: 131
Period size: 41 Copynumber: 4.1 Consensus size: 40
3684860 TTGTGACGTT
* * *
3684870 TTTTTATCAAAAACGCCGATATTGCTTACTTTTTGCGGCG
1 TTTTTATCATAAACGCCGCTACTGCTTACTTTTTGCGGCG
* * *
3684910 TTTTTCTCATAAACGCCGCTACTGC-TAGATCTTTTGCAGCG
1 TTTTTATCATAAACGCCGCTACTGCTTA-CT-TTTTGCGGCG
* * * * *
3684951 TTTTTTTTATAAACGCCGCTACTGCTTGACCTTTTGTGGCA
1 TTTTTATCATAAACGCCGCTACTGCTT-ACTTTTTGCGGCG
* * *
3684992 TTTTTA--ACAAACACCGCTACTGCTTAACCTTTTG-GTGCG
1 TTTTTATCATAAACGCCGCTACTGCTT-ACTTTTTGCG-GCG
3685031 TTTT
1 TTTT
3685035 CCTATTAGCG
Statistics
Matches: 102, Mismatches: 18, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
38 1 0.01
39 33 0.32
40 22 0.22
41 44 0.43
42 1 0.01
43 1 0.01
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (40 bp):
TTTTTATCATAAACGCCGCTACTGCTTACTTTTTGCGGCG
Found at i:3684945 original size:41 final size:41
Alignment explanation
Indices: 3684900--3685034 Score: 134
Period size: 41 Copynumber: 3.3 Consensus size: 41
3684890 ATTGCTTACT
*
3684900 TTTTGCGGCGTTTTTCTCATAAACGCCGCTACTGCTAGATC
1 TTTTGCGGCGTTTTTCTCATAAACGCCGCTACTGCTAGACC
* * * *
3684941 TTTTGCAGCGTTTTTTTTATAAACGCCGCTACTGCTTGACC
1 TTTTGCGGCGTTTTTCTCATAAACGCCGCTACTGCTAGACC
* * * * *
3684982 TTTTGTGGC-ATTTT-TAACAAACACCGCTACTGCTTA-ACC
1 TTTTGCGGCGTTTTTCTCATAAACGCCGCTACTGC-TAGACC
3685021 TTTTG-GTGCGTTTT
1 TTTTGCG-GCGTTTT
3685035 CCTATTAGCG
Statistics
Matches: 78, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
38 1 0.01
39 26 0.33
40 8 0.10
41 43 0.55
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (41 bp):
TTTTGCGGCGTTTTTCTCATAAACGCCGCTACTGCTAGACC
Found at i:3685632 original size:22 final size:22
Alignment explanation
Indices: 3685598--3685640 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3685588 TATCAAAACA
3685598 ATAATAACAAAAT-AGTAGCAAT
1 ATAATAACAAAATGA-TAGCAAT
* *
3685620 ATAATAGCGAAATGATAGCAA
1 ATAATAACAAAATGATAGCAA
3685641 AACAATGCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATGATAGCAAT
Found at i:3691310 original size:18 final size:18
Alignment explanation
Indices: 3691287--3691321 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3691277 ATTAATTAAA
*
3691287 AATTTTAAAATATAAATT
1 AATTTTAAAACATAAATT
*
3691305 AATTTTGAAACATAAAT
1 AATTTTAAAACATAAAT
3691322 ATTATTAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (18 bp):
AATTTTAAAACATAAATT
Found at i:3694697 original size:6 final size:6
Alignment explanation
Indices: 3694688--3694715 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3694678 TCGCCCATCC
3694688 CCACCT CCACCT CCACCT CCACCT CCAC
1 CCACCT CCACCT CCACCT CCACCT CCAC
3694716 TTCTAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.68, G:0.00, T:0.14
Consensus pattern (6 bp):
CCACCT
Found at i:3695731 original size:7 final size:7
Alignment explanation
Indices: 3695721--3695767 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
3695711 CATTTTACTT
3695721 TTTTATA
1 TTTTATA
3695728 TTTTATA
1 TTTTATA
*
3695735 TTTTTTA
1 TTTTATA
3695742 GTTTTAT-
1 -TTTTATA
*
3695749 GTTTATA
1 TTTTATA
3695756 TTTTA-A
1 TTTTATA
3695762 TTTTAT
1 TTTTAT
3695768 TAATAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
6 11 0.33
7 17 0.52
8 5 0.15
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.72
Consensus pattern (7 bp):
TTTTATA
Found at i:3696245 original size:25 final size:27
Alignment explanation
Indices: 3696218--3696273 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
3696208 TTATTATTCT
3696218 AAATA-TTAAAAAAAATTATAATTATA
1 AAATATTTAAAAAAAATTATAATTATA
* * *
3696244 AAATATTTTAAAAAAACTATAA-AATA
1 AAATATTTAAAAAAAATTATAATTATA
3696270 AAAT
1 AAAT
3696274 GATTCAACCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (27 bp):
AAATATTTAAAAAAAATTATAATTATA
Found at i:3707200 original size:17 final size:18
Alignment explanation
Indices: 3707168--3707208 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
3707158 TCCTAAACTA
3707168 CAATAATTCAATTTTCAC
1 CAATAATTCAATTTTCAC
*
3707186 CAATCATTC-ATTTTCAC
1 CAATAATTCAATTTTCAC
*
3707203 TAATAA
1 CAATAA
3707209 AACTGCACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.39, C:0.22, G:0.00, T:0.39
Consensus pattern (18 bp):
CAATAATTCAATTTTCAC
Found at i:3715646 original size:21 final size:21
Alignment explanation
Indices: 3715622--3715674 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
3715612 CATTGTTTCT
*
3715622 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
3715643 AATCTCACTGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
3715664 AATCTCACCGC
1 AATCTCACCGC
3715675 CACCGCTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.30, C:0.36, G:0.09, T:0.25
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:3716920 original size:21 final size:21
Alignment explanation
Indices: 3716896--3716945 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
3716886 CAATTTAGTT
*
3716896 AGATTAGTTACTGTAGCGGTG
1 AGATTAGATACTGTAGCGGTG
*
3716917 AGATTGGATACTGTAGCGGTG
1 AGATTAGATACTGTAGCGGTG
3716938 AGATTAGA
1 AGATTAGA
3716946 AACAATAGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.08, G:0.34, T:0.30
Consensus pattern (21 bp):
AGATTAGATACTGTAGCGGTG
Found at i:3732618 original size:26 final size:27
Alignment explanation
Indices: 3732572--3732624 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
3732562 TCAATTTTAA
* *
3732572 AAAAATAAATATTATTATTT-GAAAAT
1 AAAAATAAAAATGATTATTTGGAAAAT
3732598 AAAAATAGAAAATGATT-TTTGGAAAAT
1 AAAAATA-AAAATGATTATTTGGAAAAT
3732625 TTATTGTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (27 bp):
AAAAATAAAAATGATTATTTGGAAAAT
Found at i:3732734 original size:15 final size:14
Alignment explanation
Indices: 3732701--3732734 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3732691 CTAGTTGACA
3732701 ATTTTTTAAAAACT
1 ATTTTTTAAAAACT
* *
3732715 ATTTTTTGAAAATT
1 ATTTTTTAAAAACT
3732729 ATTTTT
1 ATTTTT
3732735 AATAAAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (14 bp):
ATTTTTTAAAAACT
Done.