Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 110 of 144
Found at i:25525792 original size:21 final size:20
Alignment explanation
Indices: 25525766--25525804 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
25525756 GACCGGGCCC
25525766 AAAAAATAATAAAAAAAATAA
1 AAAAAATAA-AAAAAAAATAA
*
25525787 AAAAAATAAAAATAAAAT
1 AAAAAATAAAAAAAAAAT
25525805 TCTCAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAAAATAAAAAAAAAATAA
Found at i:25531951 original size:10 final size:10
Alignment explanation
Indices: 25531936--25531962 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
25531926 TTATTTTCAA
25531936 GGAGTATCAT
1 GGAGTATCAT
25531946 GGAGTATCAT
1 GGAGTATCAT
25531956 GGAGTAT
1 GGAGTAT
25531963 TGAAGAGATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.33, T:0.30
Consensus pattern (10 bp):
GGAGTATCAT
Found at i:25532554 original size:8 final size:8
Alignment explanation
Indices: 25532534--25532581 Score: 53
Period size: 8 Copynumber: 5.8 Consensus size: 8
25532524 TTCTATCACC
25532534 AAAAAAGA
1 AAAAAAGA
25532542 TAAAAAA-A
1 -AAAAAAGA
25532550 GAAAAAAGA
1 -AAAAAAGA
*
25532559 AAAAAGGA
1 AAAAAAGA
25532567 AAAAAAGA
1 AAAAAAGA
25532575 AATAAAA
1 AA-AAAA
25532582 TAATATCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
8 23 0.68
9 11 0.32
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.04
Consensus pattern (8 bp):
AAAAAAGA
Found at i:25532725 original size:28 final size:28
Alignment explanation
Indices: 25532688--25532742 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
25532678 AAATTATAAA
*
25532688 TTTTTTATTTTAAATACTTGAAATGAAT
1 TTTTTTATTTTAAATACTTAAAATGAAT
*
25532716 TTTTTTATTTTAAATATTTAAAATGAA
1 TTTTTTATTTTAAATACTTAAAATGAA
25532743 AAATATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (28 bp):
TTTTTTATTTTAAATACTTAAAATGAAT
Found at i:25538842 original size:31 final size:29
Alignment explanation
Indices: 25538798--25538882 Score: 82
Period size: 30 Copynumber: 2.9 Consensus size: 29
25538788 AGACCTCCCA
* * **
25538798 AAATATTTCAAAATTTTCATTTTTCCTTTG
1 AAATTTTTGAAAATTTTCATTTTTCC-TCC
* *
25538828 AAATTTGTTGAAAATTTT-AATTTACCTCC
1 AAATTT-TTGAAAATTTTCATTTTTCCTCC
25538857 AAATTTTTGAAAATTTTCATTATTTC
1 AAATTTTTGAAAATTTTCATT-TTTC
25538883 TTTTAATTAT
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 11 0.25
29 9 0.20
30 14 0.32
31 10 0.23
ACGTcount: A:0.33, C:0.12, G:0.05, T:0.51
Consensus pattern (29 bp):
AAATTTTTGAAAATTTTCATTTTTCCTCC
Found at i:25547875 original size:65 final size:64
Alignment explanation
Indices: 25547762--25547953 Score: 240
Period size: 65 Copynumber: 3.0 Consensus size: 64
25547752 TTCATACGCG
* * * * * * *
25547762 ATCTCACATGTGATCTCACAGGAGGATGTAGGTACCCTTCTTGTGAACACTCAATAACATGCGCT
1 ATCTCACATGTGACCTCGCAAGAGGATGTAAGTA-CCTTCCTGCGAACACTCAATACCATGCGCT
* *
25547827 ATCTCACATGTGACCTCGCAAGAGGATGCAAGTACCTTTCCTGCGAACACTCAATACCATGTGCT
1 ATCTCACATGTGACCTCGCAAGAGGATGTAAGTACC-TTCCTGCGAACACTCAATACCATGCGCT
* * * * *
25547892 ATCTCACATGTGAGCTCGCAAGAGGATGTAAGCACCCTCCTGCAAAAACTCAATACCATGCG
1 ATCTCACATGTGACCTCGCAAGAGGATGTAAGTACCTTCCTGCGAACACTCAATACCATGCG
25547954 ATCTCGTTGC
Statistics
Matches: 110, Mismatches: 16, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
64 24 0.22
65 86 0.78
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (64 bp):
ATCTCACATGTGACCTCGCAAGAGGATGTAAGTACCTTCCTGCGAACACTCAATACCATGCGCT
Found at i:25562257 original size:31 final size:31
Alignment explanation
Indices: 25562205--25562272 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 31
25562195 TTACTACAAT
* *
25562205 TATATAT-TATATCTTCAATTAAAATTTTAAA
1 TATATATATATATATACAATT-AAATTTTAAA
*
25562236 TATATATATATATATAC-ATTAAATTTTATA
1 TATATATATATATATACAATTAAATTTTAAA
25562266 TA-ATATA
1 TATATATA
25562273 ATTTACATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 5 0.15
30 11 0.33
31 10 0.30
32 7 0.21
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (31 bp):
TATATATATATATATACAATTAAATTTTAAA
Found at i:25562290 original size:26 final size:28
Alignment explanation
Indices: 25562235--25562291 Score: 66
Period size: 26 Copynumber: 2.1 Consensus size: 28
25562225 AAAATTTTAA
*
25562235 ATATATATATATATATACATTAAATTTT
1 ATATATATATATATATACATTAAATATT
*
25562263 ATATA-ATATA-ATTTACA-TAATATATT
1 ATATATATATATATATACATTAA-ATATT
25562289 ATA
1 ATA
25562292 AAATTGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
25 3 0.12
26 13 0.50
27 5 0.19
28 5 0.19
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (28 bp):
ATATATATATATATATACATTAAATATT
Found at i:25563148 original size:29 final size:30
Alignment explanation
Indices: 25563081--25563148 Score: 70
Period size: 31 Copynumber: 2.3 Consensus size: 30
25563071 ATTGTTAGAT
25563081 TTAT-TTTTTCATATAACAAATGAAGATTTC
1 TTATATTTTTCATATAACAAATG-AGATTTC
* * *
25563111 TTTTTTTTTTCTTATAACAAATG-GATTTGC
1 TTATATTTTTCATATAACAAATGAGATTT-C
25563141 -TATATTTT
1 TTATATTTT
25563149 AGTATGTCTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 11 0.34
30 4 0.12
31 17 0.53
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.54
Consensus pattern (30 bp):
TTATATTTTTCATATAACAAATGAGATTTC
Found at i:25563978 original size:25 final size:24
Alignment explanation
Indices: 25563926--25563978 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
25563916 ATTAATTATT
** *
25563926 AATTATATATATATCTTTTACTAC
1 AATTATATATATATCTTCAACTAA
*
25563950 AATTATATATTATATCTTCAATTAA
1 AATTATATA-TATATCTTCAACTAA
25563975 AATT
1 AATT
25563979 TTAAACATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTATATATATATCTTCAACTAA
Found at i:25568369 original size:30 final size:30
Alignment explanation
Indices: 25568321--25568694 Score: 317
Period size: 30 Copynumber: 12.6 Consensus size: 30
25568311 GGAAGTTTGG
* *
25568321 GGGT-AAAATGGTAATTTTTG-AAAGTTTCA
1 GGGTCAAAAT-GTAATTTTGGAAAAGTTTTA
* *
25568350 GGGTAAAAATGTAATTTTTTGG-AAA--TTTG
1 GGGTCAAAATGTAA--TTTTGGAAAAGTTTTA
* * *
25568379 GGGTCGAAATATGATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
* *
25568409 GGGTCAAAATGTAATTTTGGAAAATTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
* *
25568439 GGGTCAAAATGTAATTTCTAG-AAAGTTTTG
1 GGGTCAAAATGTAATTT-TGGAAAAGTTTTA
* *
25568469 GGGTCAAAGTATAATTTTGGAAAAGTTTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
* * *
25568499 GGGTCAAAATATAATTTTGG-AAATTTTTG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
* * *
25568528 GGGTTAAAATATGATTTTGGAAAAG-TTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
* *
25568557 GGGGTTAAAATGTAATTTT-TAGAAAG-TTTA
1 -GGGTCAAAATGTAATTTTGGA-AAAGTTTTA
* *
25568587 GGGGTTAAAATGTAATTTT-TAGAAAG-TTTA
1 -GGGTCAAAATGTAATTTTGGA-AAAGTTTTA
* *
25568617 GGGGTCAAAATATAATTTTGGAAAAGTTTTG
1 -GGGTCAAAATGTAATTTTGGAAAAGTTTTA
*
25568648 GGGTCAAAATATAATTTTGGAAAAG-TTTA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTTA
*
25568677 GGGGT-TAAATGTAATTTT
1 -GGGTCAAAATGTAATTTT
25568695 TAGACAATTT
Statistics
Matches: 295, Mismatches: 36, Indels: 28
0.82 0.10 0.08
Matches are distributed among these distances:
27 6 0.02
28 3 0.01
29 65 0.22
30 207 0.70
31 14 0.05
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.39
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTTA
Found at i:25568473 original size:60 final size:59
Alignment explanation
Indices: 25568313--25568694 Score: 382
Period size: 60 Copynumber: 6.4 Consensus size: 59
25568303 GGATTTAGGG
* * ** * *
25568313 AAGTTTGGGGGT-AAAATGGTAATTTTTGAAAGTTTCAGGGTAAAAATGTAATTTTTTGG-A
1 AAGTTTAGGGGTCAAAAT-GTAATTTTAGAAAGTTTTGGGGTCAAAATATAA--TTTTGGAA
* * * * * *
25568373 AA-TTT-GGGGTCGAAATATGATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTAG-AAAGTTTTGGGGTCAAAATATAATTTTGGAA
* * *
25568431 AATTTTTGGGGTCAAAATGTAATTTCTAGAAAGTTTTGGGGTCAAAGTATAATTTTGGAA
1 AAGTTTAGGGGTCAAAATGTAATTT-TAGAAAGTTTTGGGGTCAAAATATAATTTTGGAA
* * * * *
25568491 AAGTTTTA-GGGTCAAAATATAATTTTGGAAATTTTTGGGGTTAAAATATGATTTTGGAA
1 AAG-TTTAGGGGTCAAAATGTAATTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGAA
* * * * *
25568550 AAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATGTAATTTT-TAGA
1 AAGTTTAGGGGTCAAAATGTAA-TTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGA-A
* *
25568610 AAGTTTAGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAA
1 AAGTTTAGGGGTCAAAATGTAATTTTAG-AAAGTTTTGGGGTCAAAATATAATTTTGGAA
*
25568670 AAGTTTAGGGGT-TAAATGTAATTTT
1 AAGTTTAGGGGTCAAAATGTAATTTT
25568695 TAGACAATTT
Statistics
Matches: 272, Mismatches: 38, Indels: 25
0.81 0.11 0.07
Matches are distributed among these distances:
57 6 0.02
58 19 0.07
59 92 0.34
60 149 0.55
61 6 0.02
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.38
Consensus pattern (59 bp):
AAGTTTAGGGGTCAAAATGTAATTTTAGAAAGTTTTGGGGTCAAAATATAATTTTGGAA
Found at i:25568538 original size:149 final size:148
Alignment explanation
Indices: 25568313--25568685 Score: 477
Period size: 149 Copynumber: 2.5 Consensus size: 148
25568303 GGATTTAGGG
* * * * * *
25568313 AAGTTTGGGGGT-AAAATGGTAATTTTTG-AAAGTTTCAGGGTAAAAATGTAATTTTTTGGAAA-
1 AAGTTTAGGGGTCAAAAT-ATAATTTTGGAAAAGTTTTAGGGTCAAAATATAA--TTTTGGAAAT
** * *
25568375 TTTGGGGTCGAAATATGATTTTGGAAAAGTTTTA-GGGTCAAAATGTAATTTTG-GAAAATTTTT
63 TTTGGGGTTAAAATATGATTTTGGAAAAG-TTTAGGGGTCAAAATGTAATTTTGAG-AAAGTTTA
25568438 GGGGTCAAAATGTAATTTCTAGA
126 GGGGTCAAAATGTAATTTCTAGA
* *
25568461 AAGTTTTGGGGTCAAAGTATAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGAAATTTT
1 AAGTTTAGGGGTCAAAATATAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGAAA-TTT
* *
25568526 TGGGGTTAAAATATGATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTTTAGGGG
65 TGGGGTTAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGAGAAAGTTTAGGGG
* *
25568591 TTAAAATGTAATTTTTAGA
130 TCAAAATGTAATTTCTAGA
*
25568610 AAGTTTAGGGGTCAAAATATAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTT
1 AAGTTTAGGGGTCAAAATATAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGG-AAA-TT
*
25568675 TAGGGGTTAAA
64 TTGGGGTTAAA
25568686 TGTAATTTTT
Statistics
Matches: 198, Mismatches: 20, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
147 9 0.05
148 23 0.12
149 150 0.76
150 16 0.08
ACGTcount: A:0.35, C:0.02, G:0.24, T:0.38
Consensus pattern (148 bp):
AAGTTTAGGGGTCAAAATATAATTTTGGAAAAGTTTTAGGGTCAAAATATAATTTTGGAAATTTT
GGGGTTAAAATATGATTTTGGAAAAGTTTAGGGGTCAAAATGTAATTTTGAGAAAGTTTAGGGGT
CAAAATGTAATTTCTAGA
Found at i:25570281 original size:20 final size:20
Alignment explanation
Indices: 25570243--25570281 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25570233 CAGGGAATGG
*
25570243 TGGAGCTTGGTGGTGGCAGA
1 TGGAGCTTGGTGGTAGCAGA
25570263 TGGAGC-TGGTGGTCAGCAG
1 TGGAGCTTGGTGGT-AGCAG
25570282 CAGCATAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.15, C:0.13, G:0.49, T:0.23
Consensus pattern (20 bp):
TGGAGCTTGGTGGTAGCAGA
Found at i:25570506 original size:28 final size:28
Alignment explanation
Indices: 25570449--25570506 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 28
25570439 TTCAGCTCAA
* * *
25570449 TTGGGCTTTTTGTAATCGGGCCTTTAAT
1 TTGGGCTTTTTGTAATCGGACATTGAAT
*
25570477 TTGGGCTTTTTGTAAAT-GGACATTGGAT
1 TTGGGCTTTTTGT-AATCGGACATTGAAT
25570505 TT
1 TT
25570507 TAATTTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.17, C:0.10, G:0.26, T:0.47
Consensus pattern (28 bp):
TTGGGCTTTTTGTAATCGGACATTGAAT
Found at i:25570550 original size:17 final size:17
Alignment explanation
Indices: 25570530--25570594 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 17
25570520 TTAATATTAT
* *
25570530 TTTAAATTAAGTTTAAA
1 TTTAAAATAAATTTAAA
25570547 TTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
*
25570564 --T-AAGTAAATTTAAA
1 TTTAAAATAAATTTAAA
*
25570578 TTTAAGATAAATTTAAA
1 TTTAAAATAAATTTAAA
25570595 AATGAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 12 0.30
15 1 0.03
16 1 0.03
17 26 0.65
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:25570557 original size:11 final size:11
Alignment explanation
Indices: 25570543--25570613 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
25570533 AAATTAAGTT
25570543 TAAATTTAAAA
1 TAAATTTAAAA
25570554 TAAATTT-AAA
1 TAAATTTAAAA
* *
25570564 T-AA-GTAAATT
1 TAAATTTAAA-A
*
25570574 TAAATTTAAGA
1 TAAATTTAAAA
25570585 TAAATTTAAAAA
1 TAAATTT-AAAA
*
25570597 TGAATTTAAAA
1 TAAATTTAAAA
*
25570608 TTAATT
1 TAAATT
25570614 CAAACTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
8 1 0.02
9 4 0.09
10 5 0.11
11 25 0.53
12 12 0.26
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:25570579 original size:31 final size:29
Alignment explanation
Indices: 25570514--25570611 Score: 99
Period size: 31 Copynumber: 3.3 Consensus size: 29
25570504 TTTTAATTTA
* * * * *
25570514 TTAAATTTAATAT-TATTTTAAATTAAGT
1 TTAAATTTAAAATAAATTTAAAAATAAAT
25570542 TTAAATTTAAAATAAATTTAAATAAGTAAAT
1 TTAAATTTAAAATAAATTTAAA-AA-TAAAT
* *
25570573 TTAAATTTAAGATAAATTTAAAAATGAAT
1 TTAAATTTAAAATAAATTTAAAAATAAAT
*
25570602 TTAAAATTAA
1 TTAAATTTAA
25570612 TTCAAACTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.20
29 19 0.32
30 3 0.05
31 25 0.42
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (29 bp):
TTAAATTTAAAATAAATTTAAAAATAAAT
Found at i:25571136 original size:31 final size:31
Alignment explanation
Indices: 25571094--25571205 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 31
25571084 TTATCCACTC
*
25571094 TACTTCGATTTCAAGAGGATGACGTTGCTCT
1 TACTTCAATTTCAAGAGGATGACGTTGCTCT
** * * *
25571125 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGAC--G-T-TGCTCT
*
25571161 CTACCTCAATTTCAAGAGGATGACGTTGCTCT
1 -TACTTCAATTTCAAGAGGATGACGTTGCTCT
25571193 TACTTCAATTTCA
1 TACTTCAATTTCA
25571206 GAGAAAAAGA
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
31 24 0.39
32 11 0.18
33 1 0.02
34 2 0.03
35 1 0.02
36 11 0.18
37 12 0.19
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (31 bp):
TACTTCAATTTCAAGAGGATGACGTTGCTCT
Found at i:25571317 original size:76 final size:76
Alignment explanation
Indices: 25571186--25571870 Score: 1129
Period size: 76 Copynumber: 9.0 Consensus size: 76
25571176 GAGGATGACG
* * * * *
25571186 TTGCTCTTACTTCAATTTCAGAGAAAAAGACGTGTTATCCACTCTACTTCGATTTCAAGCAG-TC
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGAT-
* *
25571250 AGGAAAAGATCT
65 TGGAAATGATCT
*
25571262 TTGCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
25571327 GGAAATGATCT
66 GGAAATGATCT
* *
25571338 TTGCTCCTACTTCAATTTCAGAGATGAAGACTTGTCATCCACTCTACTTCAATTTCAAGCGGATT
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
25571403 GGAAATGATCT
66 GGAAATGATCT
* *
25571414 TTGCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAACGGATT
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
*
25571479 GGAAAAGATCT
66 GGAAATGATCT
**
25571490 TTGCTCCTACTTCAATTTCAGAGATAAAGGTTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
25571555 GGAAATGATCT
66 GGAAATGATCT
* * * *
25571566 TTGCTCCTAGTTCAATTTCAGAGATGAAGACTTGCTATCTACTCTACTTCAATTTCAAGCGGATT
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
25571631 GGAAATGATCT
66 GGAAATGATCT
* *
25571642 TTGCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGAATT
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
25571707 GGAAATGATCT
66 GGAAATGATCT
* *
25571718 TTGCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTTTACTTCAATTTCAAGCGGATT
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
25571783 GGAAATGATCT
66 GGAAATGATCT
* *
25571794 TTGCTCATACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
1 TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
25571859 GGAAATGATCT
66 GGAAATGATCT
25571870 T
1 T
25571871 GTTTGGTCTG
Statistics
Matches: 573, Mismatches: 35, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
76 572 1.00
77 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (76 bp):
TTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATT
GGAAATGATCT
Found at i:25571407 original size:152 final size:152
Alignment explanation
Indices: 25570976--25571870 Score: 1268
Period size: 152 Copynumber: 6.0 Consensus size: 152
25570966 GCCTTGTCTA
* * * * * ** *
25570976 GCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAGTTTTACTTCAATTTCAAAAGGATAG
1 GCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCA-CTCTACTTCAATTTCAAGCGGATTG
* * * *
25571041 GAAATGATC-TTGCTCTTACTTCAATTTCAGAGAAAAAGACGTGTTATCCACTCTACTTCGATTT
65 GAAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTT
*
25571105 CAA---GA--GG--ATGA-CGTT
130 CAAGCGGATTGGAAATGATCTTT
* * *
25571120 GCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACCTCAATTTCAA---GA--GG
1 GCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATTGG
* * * * *
25571180 --ATGA-CGTTGCTCTTACTTCAATTTCAGAGAAAAAGACGTGTTATCCACTCTACTTCGATTTC
66 AAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTC
* * *
25571242 AAGCAG-TCAGGAAAAGATCTTT
131 AAGCGGAT-TGGAAATGATCTTT
*
25571264 GCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCTACTTCAATTTCAAGCGGATTGG
1 GCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATTGG
* *
25571329 AAATGATCTTTGCTCCTACTTCAATTTCAGAGATGAAGACTTGTCATCCACTCTACTTCAATTTC
66 AAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTC
25571394 AAGCGGATTGGAAATGATCTTT
131 AAGCGGATTGGAAATGATCTTT
* *
25571416 GCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAACGGATTGG
1 GCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATTGG
* **
25571481 AAAAGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGGTTTGTTATCCACTCTACTTCAATTTC
66 AAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTC
25571546 AAGCGGATTGGAAATGATCTTT
131 AAGCGGATTGGAAATGATCTTT
* * * *
25571568 GCTCCTAGTTCAATTTCAGAGATGAAGACTTGCTATCTACTCTACTTCAATTTCAAGCGGATTGG
1 GCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATTGG
*
25571633 AAATGATCTTTGCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTC
66 AAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTC
*
25571698 AAGCGAATTGGAAATGATCTTT
131 AAGCGGATTGGAAATGATCTTT
* *
25571720 GCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTTTACTTCAATTTCAAGCGGATTGG
1 GCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATTGG
* *
25571785 AAATGATCTTTGCTCATACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCTACTTCAATTTC
66 AAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTC
25571850 AAGCGGATTGGAAATGATCTT
131 AAGCGGATTGGAAATGATCTT
25571871 GTTTGGTCTG
Statistics
Matches: 683, Mismatches: 49, Indels: 30
0.90 0.06 0.04
Matches are distributed among these distances:
135 1 0.00
136 62 0.09
138 2 0.00
139 1 0.00
140 2 0.00
141 2 0.00
143 17 0.02
144 91 0.13
147 2 0.00
149 2 0.00
151 4 0.01
152 496 0.73
153 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (152 bp):
GCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGGATTGG
AAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTTATCCACTCTACTTCAATTTC
AAGCGGATTGGAAATGATCTTT
Found at i:25571514 original size:228 final size:228
Alignment explanation
Indices: 25570976--25571870 Score: 1288
Period size: 228 Copynumber: 4.0 Consensus size: 228
25570966 GCCTTGTCTA
* * * * *
25570976 GCTCTTACTTCAATTTCAGAGATGAAGACTTGATATCCAGTTTTACTTCAATTTCAAAAGGATAG
1 GCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCA-CTCTACTTCAATTTCAAACGGATAG
* * * ** *
25571041 GAAATGATC-TTGCTCTTACTTCAATTTCAGAGAAAAAGACGTGTTATCCACTCTACTTCGATTT
65 GAAAAGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCTACTTCAATTT
* * * *
25571105 CAA---GA--GG--ATGA-CGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
130 CAAGCGGATTGGAAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTCATCCACTC
* *
25571162 TACCTCAATTTCAA---GA--GG--ATGA-CGTT
195 TACTTCAATTTCAAGCGGATTGGAAATGATCTTT
* ** * * * *
25571188 GCTCTTACTTCAATTTCAGAGAAAAAGACGTGTTATCCACTCTACTTCGATTTCAAGCAG-TCAG
1 GCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAACGGAT-AG
25571252 GAAAAGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCTACTTCAATTT
65 GAAAAGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCTACTTCAATTT
*
25571317 CAAGCGGATTGGAAATGATCTTTGCTCCTACTTCAATTTCAGAGATGAAGACTTGTCATCCACTC
130 CAAGCGGATTGGAAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTCATCCACTC
25571382 TACTTCAATTTCAAGCGGATTGGAAATGATCTTT
195 TACTTCAATTTCAAGCGGATTGGAAATGATCTTT
*
25571416 GCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAACGGATTGG
1 GCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAACGGATAGG
*
25571481 AAAAGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGGTTTGTTATCCACTCTACTTCAATTTC
66 AAAAGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCTACTTCAATTTC
* * *
25571546 AAGCGGATTGGAAATGATCTTTGCTCCTAGTTCAATTTCAGAGATGAAGACTTG-CTATCTACTC
131 AAGCGGATTGGAAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTC-ATCCACTC
25571610 TACTTCAATTTCAAGCGGATTGGAAATGATCTTT
195 TACTTCAATTTCAAGCGGATTGGAAATGATCTTT
* * *
25571644 GCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAGCGAATTGG
1 GCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAACGGATAGG
* *
25571709 AAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTTTACTTCAATTTC
66 AAAAGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCTACTTCAATTTC
* * *
25571774 AAGCGGATTGGAAATGATCTTTGCTCATACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCT
131 AAGCGGATTGGAAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTCATCCACTCT
25571839 ACTTCAATTTCAAGCGGATTGGAAATGATCTT
196 ACTTCAATTTCAAGCGGATTGGAAATGATCTT
25571871 GTTTGGTCTG
Statistics
Matches: 617, Mismatches: 45, Indels: 26
0.90 0.07 0.04
Matches are distributed among these distances:
210 1 0.00
211 25 0.04
212 88 0.14
215 2 0.00
217 2 0.00
219 4 0.01
220 54 0.09
223 2 0.00
225 2 0.00
227 5 0.01
228 431 0.70
229 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (228 bp):
GCTCCTACTTCAATTTCAGAGATGAAGACTTGTTATCCACTCTACTTCAATTTCAAACGGATAGG
AAAAGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGATTTGTTATCCACTCTACTTCAATTTC
AAGCGGATTGGAAATGATCTTTGCTCCTACTTCAATTTCAGAGATAAAGACTTGTCATCCACTCT
ACTTCAATTTCAAGCGGATTGGAAATGATCTTT
Found at i:25583250 original size:30 final size:29
Alignment explanation
Indices: 25583213--25583771 Score: 451
Period size: 30 Copynumber: 18.7 Consensus size: 29
25583203 GGTAAAATGG
* *
25583213 TAATTTTT-GAAAGTTTCAGGGTAAAAATG
1 TAATTTTTAGAAAGTTT-AGGGTCAAAATA
* * *
25583242 TAATTTTTTGGAAA-TTTGGGGTCGAAATA
1 TAA-TTTTTAGAAAGTTTAGGGTCAAAATA
** * *
25583271 CGA-TTTTGGAAAAGTTTTAGGGTCAAAATG
1 TAATTTTTAG-AAAG-TTTAGGGTCAAAATA
* * * *
25583301 TAA-TTTTGGAAAAGTTTTGGGGTTAAAATG
1 TAATTTTTAG-AAAG-TTTAGGGTCAAAATA
* *
25583331 TAATTTCTAGAAAGTTTTAGGGTCAAAGTA
1 TAATTTTTAGAAAG-TTTAGGGTCAAAATA
* *
25583361 TAA-TTTTGGAAAAGTTTTAGGGTTAAAA-A
1 TAATTTTTAG-AAAG-TTTAGGGTCAAAATA
* * *
25583390 TAA-TTTTGGAAAAGTTTAGGGGTTAAAAATG
1 TAATTTTTAG-AAAGTTTA-GGG-TCAAAATA
*
25583421 TAATTTTTAGAAAGTTTAGGGGGTTAAAATA
1 TAATTTTTAGAAAGTTTA--GGGTCAAAATA
* *
25583452 TAATTTTTAGAAAGCTTAGGGGTCAAAATG
1 TAATTTTTAGAAAGTTTA-GGGTCAAAATA
*
25583482 TAATTTTTAGAAAGTTTAGGGGTTAAAATA
1 TAATTTTTAGAAAGTTTA-GGGTCAAAATA
*
25583512 TAA-TTTTAGAAAAGTTTTGAGGTCAAAATA
1 TAATTTTTAG-AAAGTTTAG-GGTCAAAATA
* *
25583542 TAA-TTTTGGAAAAGTTTAGGGGTCAAAATG
1 TAATTTTTAG-AAAGTTTA-GGGTCAAAATA
* *
25583572 TAATTTTTAGAAAGTTTAGGGGTTAAAATG
1 TAATTTTTAGAAAGTTTA-GGGTCAAAATA
25583602 TAATTTTTAGAAAGTTTAGGGGTCAAAATA
1 TAATTTTTAGAAAGTTTA-GGGTCAAAATA
*
25583632 TAATTTTTAGAAAGTTTTGGGGTCAAAATA
1 TAATTTTTAGAAAG-TTTAGGGTCAAAATA
*
25583662 TAATTTTTAGAAAGTTTAAGGGTTAAAATA
1 TAATTTTTAGAAAGTTT-AGGGTCAAAATA
* *
25583692 TAA-TTTTAGAAAAGTTTTGGGGTTAAAATA
1 TAATTTTTAG-AAAG-TTTAGGGTCAAAATA
* *
25583722 TAA-TTTTGGAAAAGTTTAGGAGTC-AAATG
1 TAATTTTTAG-AAAGTTTAGG-GTCAAAATA
25583751 TAATTTTTAGACAA-TTTAGGG
1 TAATTTTTAGA-AAGTTTAGGG
25583772 ACTTACAAAG
Statistics
Matches: 455, Mismatches: 52, Indels: 47
0.82 0.09 0.08
Matches are distributed among these distances:
27 6 0.01
28 8 0.02
29 69 0.15
30 309 0.68
31 54 0.12
32 9 0.02
ACGTcount: A:0.38, C:0.03, G:0.22, T:0.38
Consensus pattern (29 bp):
TAATTTTTAGAAAGTTTAGGGTCAAAATA
Found at i:25583350 original size:60 final size:59
Alignment explanation
Indices: 25583194--25583741 Score: 512
Period size: 60 Copynumber: 9.2 Consensus size: 59
25583184 GGATTTAAGG
* * * * *
25583194 AAGTTT-GGGGGTAAAATGGTAATTTTTGAAAGTTTCAGGGTAAAAATGTAATTTTTTGG-A
1 AAGTTTAGGGGTTAAAAT-ATAATTTTAGAAAGTTTTAGGGTCAAAATGTAA--TTTTGGAA
** ** *
25583254 AA-TTT-GGGGTCGAAATACGATTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTGGAA
1 AAGTTTAGGGGTTAAAATATAATTTTAG-AAAGTTTTAGGGTCAAAATGTAATTTTGGAA
* * * *
25583312 AAGTTTTGGGGTTAAAATGTAATTTCTAGAAAGTTTTAGGGTCAAAGTATAATTTTGGAA
1 AAGTTTAGGGGTTAAAATATAATTT-TAGAAAGTTTTAGGGTCAAAATGTAATTTTGGAA
* * *
25583372 AAGTTTTA-GGGTTAAAA-ATAATTTTGGAAAAG-TTTAGGGGTTAAAAATGTAATTTT-TAGA
1 AAG-TTTAGGGGTTAAAATATAATTTTAG-AAAGTTTTA-GGG-TCAAAATGTAATTTTGGA-A
* *
25583432 AAGTTTAGGGGGTTAAAATATAATTTTTAGAAAG-CTTAGGGGTCAAAATGTAATTTT-TAGA
1 AAGTTTA-GGGGTTAAAATATAA-TTTTAGAAAGTTTTA-GGGTCAAAATGTAATTTTGGA-A
*
25583493 AAGTTTAGGGGTTAAAATATAATTTTAGAAAAGTTTT-GAGGTCAAAATATAATTTTGGAA
1 AAGTTTAGGGGTTAAAATATAATTTTAG-AAAGTTTTAG-GGTCAAAATGTAATTTTGGAA
* * * *
25583553 AAGTTTAGGGGTCAAAATGTAATTTTTAGAAAG-TTTAGGGGTTAAAATGTAATTTT-TAGA
1 AAGTTTAGGGGTTAAAATATAA-TTTTAGAAAGTTTTA-GGGTCAAAATGTAATTTTGGA-A
* * * *
25583613 AAGTTTAGGGGTCAAAATATAATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTT-TAGA
1 AAGTTTAGGGGTTAAAATATAA-TTTTAGAAAGTTTTAGGGTCAAAATGTAATTTTGGA-A
* * * *
25583673 AAGTTTAAGGGTTAAAATATAATTTTAGAAAAGTTTTGGGGTTAAAATATAATTTTGGAA
1 AAGTTTAGGGGTTAAAATATAATTTTAG-AAAGTTTTAGGGTCAAAATGTAATTTTGGAA
25583733 AAGTTTAGG
1 AAGTTTAGG
25583742 AGTCAAATGT
Statistics
Matches: 419, Mismatches: 44, Indels: 50
0.82 0.09 0.10
Matches are distributed among these distances:
57 6 0.01
58 15 0.04
59 70 0.17
60 255 0.61
61 53 0.13
62 15 0.04
63 5 0.01
ACGTcount: A:0.38, C:0.02, G:0.23, T:0.37
Consensus pattern (59 bp):
AAGTTTAGGGGTTAAAATATAATTTTAGAAAGTTTTAGGGTCAAAATGTAATTTTGGAA
Found at i:25583377 original size:90 final size:88
Alignment explanation
Indices: 25583202--25583771 Score: 603
Period size: 90 Copynumber: 6.4 Consensus size: 88
25583192 GGAAGTTTGG
* * *
25583202 GGGT-AAAATGGTAATTTTT-GAAAGTTTCA-GGGTAAAAATGTAATTTTTTGGAAA--TTTGGG
1 GGGTCAAAAT-GTAATTTTTAGAAAGTTT-AGGGGTTAAAATGTAA--TTTTAGAAAGTTTTAGG
* **
25583262 GTCGAAATACGATTTTGGAAAAGTTTTA
62 GTCAAAATATAATTTTGGAAAAG-TTTA
* *
25583290 GGGTCAAAATGTAA-TTTTGGAAAAGTTTTGGGGTTAAAATGTAATTTCTAGAAAGTTTTAGGGT
1 GGGTCAAAATGTAATTTTTAG-AAAGTTTAGGGGTTAAAATGTAATTT-TAGAAAGTTTTAGGGT
*
25583354 CAAAGTATAATTTTGGAAAAGTTTTA
64 CAAAATATAATTTTGGAAAAG-TTTA
* * *
25583380 GGGTTAAAA-ATAA-TTTTGGAAAAGTTTAGGGGTTAAAAATGTAATTTTTAGAAAG-TTTAGGG
1 GGGTCAAAATGTAATTTTTAG-AAAGTTTAGGGGTT-AAAATGTAA-TTTTAGAAAGTTTTA--G
* * *
25583442 GGTTAAAATATAATTTT-TAGAAAGCTTA
61 GGTCAAAATATAATTTTGGA-AAAGTTTA
*
25583470 GGGGTCAAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATATAATTTTAGAAAAGTTTT-GAGG
1 -GGGTCAAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTAG-AAAGTTTTAG-GG
25583534 TCAAAATATAATTTTGGAAAAGTTTA
63 TCAAAATATAATTTTGGAAAAGTTTA
25583560 GGGGTCAAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAG-TTTAGGGG
1 -GGGTCAAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATGTAA-TTTTAGAAAGTTTTA-GGG
* *
25583624 TCAAAATATAATTTT-TAGAAAGTTTTG
63 TCAAAATATAATTTTGGA-AAAG-TTTA
* * * * *
25583651 GGGTCAAAATATAATTTTTAGAAAGTTTAAGGGTTAAAATATAATTTTAGAAAAGTTTTGGGGTT
1 GGGTCAAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTAG-AAAGTTTTAGGGTC
25583716 AAAATATAATTTTGGAAAAGTTTA
65 AAAATATAATTTTGGAAAAGTTTA
25583740 GGAGTC-AAATGTAATTTTTAGACAA-TTTAGGG
1 GG-GTCAAAATGTAATTTTTAGA-AAGTTTAGGG
25583772 ACTTACAAAG
Statistics
Matches: 419, Mismatches: 34, Indels: 57
0.82 0.07 0.11
Matches are distributed among these distances:
87 7 0.02
88 14 0.03
89 89 0.21
90 226 0.54
91 58 0.14
92 20 0.05
93 5 0.01
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.37
Consensus pattern (88 bp):
GGGTCAAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATGTAATTTTAGAAAGTTTTAGGGTCA
AAATATAATTTTGGAAAAGTTTA
Found at i:25583759 original size:60 final size:61
Alignment explanation
Indices: 25583274--25583761 Score: 536
Period size: 60 Copynumber: 8.1 Consensus size: 61
25583264 CGAAATACGA
* * * * *
25583274 TTTTGGAAAAGTTTTAGGGTCAAAATGTAATTTTG-GAAAAGTTTTGGGGTTAAAATGTAAT
1 TTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTGAG-AAAGTTTAGGGGTTAAAATATAAT
* * *
25583335 TTCTAG-AAAGTTTTAGGGTCAAAGTATAATTTTG-GAAAAGTTTTA-GGGTTAAAA-ATAA-
1 TTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTGAG-AAAG-TTTAGGGGTTAAAATATAAT
* * * * *
25583393 TTTTGGAAAAGTTTAGGGGTTAAAAATGTAATTTTTAGAAAGTTTAGGGGGTTAAAATATAAT
1 TTTTAGAAAAGTTTTGGGG-TCAAAATATAATTTTGAGAAAGTTTA-GGGGTTAAAATATAAT
* * * *
25583456 TTTTAG-AAAGCTTAGGGGTCAAAATGTAATTTTTAGAAAGTTTAGGGGTTAAAATATAA-
1 TTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTGAGAAAGTTTAGGGGTTAAAATATAAT
* * *
25583515 TTTTAGAAAAGTTTTGAGGTCAAAATATAATTTTG-GAAAAGTTTAGGGGTCAAAATGTAAT
1 TTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTGAG-AAAGTTTAGGGGTTAAAATATAAT
* * * * *
25583576 TTTTAG-AAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTTTAGGGGTCAAAATATAAT
1 TTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTGAGAAAGTTTAGGGGTTAAAATATAAT
* *
25583636 TTTTAG-AAAGTTTTGGGGTCAAAATATAATTTTTAGAAAGTTTAAGGGTTAAAATATAA-
1 TTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTGAGAAAGTTTAGGGGTTAAAATATAAT
* * * *
25583695 TTTTAGAAAAGTTTTGGGGTTAAAATATAATTTTG-GAAAAGTTTAGGAG-TCAAATGTAAT
1 TTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTGAG-AAAGTTTAGGGGTTAAAATATAAT
25583755 TTTTAGA
1 TTTTAGA
25583762 CAATTTAGGG
Statistics
Matches: 371, Mismatches: 41, Indels: 31
0.84 0.09 0.07
Matches are distributed among these distances:
58 4 0.01
59 39 0.11
60 259 0.70
61 49 0.13
62 15 0.04
63 5 0.01
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (61 bp):
TTTTAGAAAAGTTTTGGGGTCAAAATATAATTTTGAGAAAGTTTAGGGGTTAAAATATAAT
Found at i:25585575 original size:28 final size:28
Alignment explanation
Indices: 25585521--25585575 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
25585511 AGCCCAATTA
* *
25585521 GGCTTTTTGTAATCGGGCATTTAATTTG
1 GGCTTTTTGTAATCGGACATTGAATTTG
*
25585549 GGCTTTTTGTAAAT-GGACATTGGATTT
1 GGCTTTTTGT-AATCGGACATTGAATTT
25585576 TAATTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.45
Consensus pattern (28 bp):
GGCTTTTTGTAATCGGACATTGAATTTG
Found at i:25585619 original size:17 final size:17
Alignment explanation
Indices: 25585599--25585663 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 17
25585589 TTAATATTAT
* *
25585599 TTTAAATTAAGTTTAAA
1 TTTAAAATAAATTTAAA
25585616 TTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
*
25585633 --T-AAGTAAATTTAAA
1 TTTAAAATAAATTTAAA
*
25585647 TTTAAGATAAATTTAAA
1 TTTAAAATAAATTTAAA
25585664 AATGAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
14 12 0.30
15 1 0.03
16 1 0.03
17 26 0.65
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.42
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:25585626 original size:11 final size:11
Alignment explanation
Indices: 25585612--25585682 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
25585602 AAATTAAGTT
25585612 TAAATTTAAAA
1 TAAATTTAAAA
25585623 TAAATTT-AAA
1 TAAATTTAAAA
* *
25585633 T-AA-GTAAATT
1 TAAATTTAAA-A
*
25585643 TAAATTTAAGA
1 TAAATTTAAAA
25585654 TAAATTTAAAAA
1 TAAATTT-AAAA
*
25585666 TGAATTTAAAA
1 TAAATTTAAAA
*
25585677 TTAATT
1 TAAATT
25585683 CAAACTTTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 10
0.72 0.12 0.15
Matches are distributed among these distances:
8 1 0.02
9 4 0.09
10 5 0.11
11 25 0.53
12 12 0.26
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:25585648 original size:31 final size:29
Alignment explanation
Indices: 25585583--25585680 Score: 99
Period size: 31 Copynumber: 3.3 Consensus size: 29
25585573 TTTTAATTTA
* * * * *
25585583 TTAAATTTAATAT-TATTTTAAATTAAGT
1 TTAAATTTAAAATAAATTTAAAAATAAAT
25585611 TTAAATTTAAAATAAATTTAAATAAGTAAAT
1 TTAAATTTAAAATAAATTTAAA-AA-TAAAT
* *
25585642 TTAAATTTAAGATAAATTTAAAAATGAAT
1 TTAAATTTAAAATAAATTTAAAAATAAAT
*
25585671 TTAAAATTAA
1 TTAAATTTAA
25585681 TTCAAACTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
28 12 0.20
29 19 0.32
30 3 0.05
31 25 0.42
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (29 bp):
TTAAATTTAAAATAAATTTAAAAATAAAT
Found at i:25589455 original size:17 final size:17
Alignment explanation
Indices: 25589384--25589471 Score: 86
Period size: 17 Copynumber: 5.1 Consensus size: 17
25589374 CCTTATTTTA
25589384 ATTTTAAATTTAAAATT
1 ATTTTAAATTTAAAATT
* *
25589401 AAATTTTAAATTTGAATTT
1 --ATTTTAAATTTAAAATT
* * * *
25589420 AATTTAAGTTTGAATTT
1 ATTTTAAATTTAAAATT
*
25589437 ATTTTAAATCTAAAATT
1 ATTTTAAATTTAAAATT
*
25589454 ATTATAAATTTAAAATT
1 ATTTTAAATTTAAAATT
25589471 A
1 A
25589472 ATAAAATGTC
Statistics
Matches: 58, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
17 43 0.74
19 15 0.26
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTTAAATTTAAAATT
Found at i:25589467 original size:6 final size:6
Alignment explanation
Indices: 25589380--25589472 Score: 59
Period size: 6 Copynumber: 15.8 Consensus size: 6
25589370 TTAGCCTTAT
* * * *
25589380 TTTAAT TTTAAA TTTAAA ATTAAA TTTTAAA TTTGAA TTT-AA TTTAAG
1 TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
25589428 TTTGAA TTT-AT TTTAAA TCTAAA ATT--A TTATAAA TTTAAA ATTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA TTTAA
25589473 TAAAATGTCC
Statistics
Matches: 67, Mismatches: 14, Indels: 12
0.72 0.15 0.13
Matches are distributed among these distances:
4 2 0.03
5 10 0.15
6 47 0.70
7 8 0.12
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:25591415 original size:29 final size:29
Alignment explanation
Indices: 25591371--25591683 Score: 210
Period size: 29 Copynumber: 10.8 Consensus size: 29
25591361 CCTTAAATTG
*
25591371 TCCAAAAATTACATTTTGACCCCTGAACT
1 TCCAAAAATTACATTTTGACCCCTAAACT
* *
25591400 TTCAAAAATTCCATTTTTGA-CCCTAAAACT
1 TCCAAAAATTACA-TTTTGACCCCT-AAACT
* * *
25591430 TCCAAAAATTATATTTTTACCCCTGAACT
1 TCCAAAAATTACATTTTGACCCCTAAACT
* * * **
25591459 TCCAAAAACTATATTTTTG-CTCAAAAACT
1 TCCAAAAATTACA-TTTTGACCCCTAAACT
*
25591488 TCCAAAAATTACATTTTGACCCCAAAACT
1 TCCAAAAATTACATTTTGACCCCTAAACT
* * *
25591517 TCCAAAAATTATACTTT-A-CCCTAAAAT
1 TCCAAAAATTACATTTTGACCCCTAAACT
* *
25591544 TCCAAAAATT-CTATTTTAACCCTCGAAACT
1 TCCAAAAATTAC-ATTTTGACCC-CTAAACT
* * * *
25591574 TTCAAAAATTATATTTTTA-CCCTCAAAAT
1 TCCAAAAATTACATTTTGACCCCT-AAACT
* * * * * *
25591603 CCCAAAAATTCCATTTTTACCCTTGAATT
1 TCCAAAAATTACATTTTGACCCCTAAACT
* * * *
25591632 TCTAAAAAATCCGTTTTGA-CCCTAAAACT
1 TCCAAAAATTACATTTTGACCCCT-AAACT
*
25591661 TACAAAAATTACCATTTT-ACCCC
1 TCCAAAAATTA-CATTTTGACCCC
25591684 CAGATGTCTA
Statistics
Matches: 218, Mismatches: 51, Indels: 29
0.73 0.17 0.10
Matches are distributed among these distances:
27 21 0.10
28 11 0.05
29 127 0.58
30 59 0.27
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTACATTTTGACCCCTAAACT
Found at i:25591510 original size:58 final size:57
Alignment explanation
Indices: 25591371--25591683 Score: 269
Period size: 58 Copynumber: 5.4 Consensus size: 57
25591361 CCTTAAATTG
* **
25591371 TCCAAAAATTACATTTTGACCCCTGAACTTTCAAAAATTCCATTTTTGACCCTAAAACT
1 TCCAAAAATTACATTTTGACCCCTGAACTTCCAAAAATTATATTTTTG-CCCTAAAA-T
* * * * *
25591430 TCCAAAAATTATATTTTTACCCCTGAACTTCCAAAAACTATATTTTTGCTCAAAAACT
1 TCCAAAAATTACATTTTGACCCCTGAACTTCCAAAAATTATATTTTTGCCCTAAAA-T
** * *
25591488 TCCAAAAATTACATTTTGACCCCAAAACTTCCAAAAATTATA-CTTTACCCTAAAAT
1 TCCAAAAATTACATTTTGACCCCTGAACTTCCAAAAATTATATTTTTGCCCTAAAAT
* * *
25591544 TCCAAAAATT-CTATTTT-AACCCTCGAAACTTTCAAAAATTATATTTTTACCCTCAAAAT
1 TCCAAAAATTAC-ATTTTGACCCCT-G-AACTTCCAAAAATTATATTTTTGCCCT-AAAAT
* * * * * * **
25591603 CCCAAAAATTCCATTTTTACCCTTGAATTTCTAAAAA--ATCCGTTTTGACCCTAAAACT
1 TCCAAAAATTACATTTTGACCCCTGAACTTCCAAAAATTAT-ATTTTTG-CCCTAAAA-T
*
25591661 TACAAAAATTACCATTTT-ACCCC
1 TCCAAAAATTA-CATTTTGACCCC
25591684 CAGATGTCTA
Statistics
Matches: 208, Mismatches: 35, Indels: 23
0.78 0.13 0.09
Matches are distributed among these distances:
55 5 0.02
56 18 0.09
57 33 0.16
58 79 0.38
59 68 0.33
60 5 0.02
ACGTcount: A:0.38, C:0.25, G:0.03, T:0.34
Consensus pattern (57 bp):
TCCAAAAATTACATTTTGACCCCTGAACTTCCAAAAATTATATTTTTGCCCTAAAAT
Found at i:25595940 original size:22 final size:22
Alignment explanation
Indices: 25595897--25595941 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
25595887 TTGTACAAAG
* *
25595897 AAAAACTCAAGTATCAATCTGA
1 AAAAACTCAAGTACCAAACTGA
*
25595919 AAAAACTCAATTACCAAACTGA
1 AAAAACTCAAGTACCAAACTGA
25595941 A
1 A
25595942 CATTTTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.53, C:0.20, G:0.07, T:0.20
Consensus pattern (22 bp):
AAAAACTCAAGTACCAAACTGA
Found at i:25599820 original size:21 final size:21
Alignment explanation
Indices: 25599794--25599835 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
25599784 TAAACAATGA
* *
25599794 CAAAAAATATCGATACCTTTT
1 CAAAAAATATCAATACATTTT
*
25599815 CAAAAAGTATCAATACATTTT
1 CAAAAAATATCAATACATTTT
25599836 ATCATGTATT
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:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (21 bp):
CAAAAAATATCAATACATTTT
Found at i:25601759 original size:40 final size:40
Alignment explanation
Indices: 25601704--25601859 Score: 188
Period size: 40 Copynumber: 3.9 Consensus size: 40
25601694 AAGTTATGTT
*
25601704 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATGCGTCAG
1 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATGAGTCAG
* *
25601744 TGATAAAGTTCAAGCTACGGCTTAACAGGCTATGAG-CTG
1 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATGAGTCAG
* * * * **
25601783 ATGATAAAGTTCAAGTTATGACTTAGCGGGCTATGAGTTGG
1 -TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATGAGTCAG
* * *
25601824 TGATAAAATACAAGCTACGGCTTAGCAAGCTATGAG
1 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATGAG
25601860 CCGGTGTTAA
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
39 2 0.02
40 94 0.97
41 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (40 bp):
TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATGAGTCAG
Found at i:25601838 original size:80 final size:80
Alignment explanation
Indices: 25601704--25601860 Score: 215
Period size: 80 Copynumber: 2.0 Consensus size: 80
25601694 AAGTTATGTT
* * * *
25601704 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATGCGTCAGTGATAAAGTTCAAGCTACGGCTTAA
1 TGATAAAGTTCAAGCTACGACTTAGCAGGCTATGAGTCAGTGATAAAATACAAGCTACGGCTTAA
*
25601769 CAGGCTATGAGCTGA
66 CAAGCTATGAGCTGA
* * * ** *
25601784 TGATAAAGTTCAAGTTATGACTTAGCGGGCTATGAGTTGGTGATAAAATACAAGCTACGGCTTAG
1 TGATAAAGTTCAAGCTACGACTTAGCAGGCTATGAGTCAGTGATAAAATACAAGCTACGGCTTAA
25601849 CAAGCTATGAGC
66 CAAGCTATGAGC
25601861 CGGTGTTAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (80 bp):
TGATAAAGTTCAAGCTACGACTTAGCAGGCTATGAGTCAGTGATAAAATACAAGCTACGGCTTAA
CAAGCTATGAGCTGA
Found at i:25601871 original size:40 final size:40
Alignment explanation
Indices: 25601704--25601878 Score: 179
Period size: 40 Copynumber: 4.4 Consensus size: 40
25601694 AAGTTATGTT
* * * *
25601704 TGATAAAGTTCAAGCTACGGCTTAGCAGGCTATGCGTCAG
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
* * * *
25601744 TGATAAAGTTCAAGCTACGGCTTAACAGGCTATGAGCTGA
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
* * * * * **
25601784 TGATAAAGTTCAAGTTATGACTTAGCGGGCTATGAGTTGG
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
* *
25601824 TGATAAAATACAAGCTACGGCTTAGCAAGCTATGAGCCGG
1 TGATAAAATTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
* *
25601864 TGTTAAAACTCAAGC
1 TGATAAAATTCAAGC
25601879 CAAGTCATGG
Statistics
Matches: 110, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 110 1.00
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (40 bp):
TGATAAAATTCAAGCTACGGCTTAGCAGGCTATGAGCCGG
Found at i:25604444 original size:3 final size:3
Alignment explanation
Indices: 25604436--25604474 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
25604426 TCACATGTAA
25604436 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
25604475 TCTCAACGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:25613150 original size:32 final size:29
Alignment explanation
Indices: 25613085--25613151 Score: 73
Period size: 32 Copynumber: 2.2 Consensus size: 29
25613075 TTAAAATCTT
* *
25613085 TAAAAATGAAAAAAAATATACAATATTAT
1 TAAAAATGAAAAAAAATATAAAATATTAC
25613114 TAAAAATAGAAAAATAAAATATAAAA-ATTTAC
1 TAAAAAT-G-AAAA-AAAATATAAAATA-TTAC
25613146 TAAAAA
1 TAAAAA
25613152 AATTAAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
29 7 0.22
30 1 0.03
31 5 0.16
32 19 0.59
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (29 bp):
TAAAAATGAAAAAAAATATAAAATATTAC
Found at i:25613193 original size:17 final size:17
Alignment explanation
Indices: 25613159--25613191 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
25613149 AAAAATTAAA
25613159 AATATATTAGAAATTTT
1 AATATATTAGAAATTTT
*
25613176 AATAT-TTATAAATTTT
1 AATATATTAGAAATTTT
25613192 TATAAATCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (17 bp):
AATATATTAGAAATTTT
Found at i:25614458 original size:28 final size:30
Alignment explanation
Indices: 25614426--25614489 Score: 82
Period size: 28 Copynumber: 2.2 Consensus size: 30
25614416 AAAATATGTT
*
25614426 AAATTTTACCAT-ATTA-ATTATTAT-GTAA
1 AAATTTTA-CATAAATATATTATTATAGTAA
25614454 AAA-TTTACATAAATATATTATTATAGTAA
1 AAATTTTACATAAATATATTATTATAGTAA
25614483 AAATTTT
1 AAATTTT
25614490 GTTGAGCAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 3 0.10
27 7 0.23
28 11 0.35
29 7 0.23
30 3 0.10
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (30 bp):
AAATTTTACATAAATATATTATTATAGTAA
Found at i:25617446 original size:4 final size:4
Alignment explanation
Indices: 25617437--25617464 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
25617427 TACAAATCCA
25617437 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC
25617465 ATTATATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:25617583 original size:6 final size:6
Alignment explanation
Indices: 25617572--25617605 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
25617562 ACACAATCAG
*
25617572 ATTTGA ATTTGA ATATGA ATTTGA ATTTGA ATTT
1 ATTTGA ATTTGA ATTTGA ATTTGA ATTTGA ATTT
25617606 ACTATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (6 bp):
ATTTGA
Found at i:25621249 original size:51 final size:52
Alignment explanation
Indices: 25621159--25621258 Score: 123
Period size: 51 Copynumber: 1.9 Consensus size: 52
25621149 AATCAAAGAC
* * * *
25621159 ATAGTAAAAACTCGAAATTTATAAGTTGAGTGTTTTAAATATAATTGAATTG
1 ATAGTAAAAACTCAAAAATTATAAGTTGAGTGCTCTAAATATAATTGAATTG
* *
25621211 ATAGTGAAAACTCAAAAATT-TAAGTTG-GATGCTCTAAATGTAATTGAA
1 ATAGTAAAAACTCAAAAATTATAAGTTGAG-TGCTCTAAATATAATTGAA
25621259 CTGAGTTTAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
50 1 0.02
51 23 0.56
52 17 0.41
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (52 bp):
ATAGTAAAAACTCAAAAATTATAAGTTGAGTGCTCTAAATATAATTGAATTG
Found at i:25621955 original size:194 final size:198
Alignment explanation
Indices: 25621619--25622010 Score: 666
Period size: 194 Copynumber: 2.0 Consensus size: 198
25621609 ATTTTCCCTA
*
25621619 CAAATCTATACAATCTATATACATATAGTATATATGACCTTCCTGTTAACACGTGTAGACTACCA
1 CAAATCTATACAATCTATATACATATAGTATATATGACCTTCCTGTTAACACGTGTAGACCACCA
* *
25621684 TAATTCTCCATTTCCTCTTTATTTTTGGCATTTTATAAAATGATTAACTTCCAGTTTTGGTCCTT
66 TAATTCTCCATTTCCTCTTTATTTTTGGAATTTTATAAAATGATTAAATTCCAGTTTTGGTCCTT
*
25621749 TTAACATGCCTAAATTAGAGATGTCATCAATATACTTTATTTTTAACAGAATTTAGTCCCCATTT
131 TTAACATGCCTAAATTAGAGATGTAATCAATATACTTTATTTTTAACAGAATTTAGTCCCCATTT
25621814 TTT
196 TTT
* * *
25621817 CAAATCTATACAATCTATATACATATATTATATATGACCTTCCTGTTGACACGTGTATACCA-CA
1 CAAATCTATACAATCTATATACATATAGTATATATGACCTTCCTGTTAACACGTGTAGACCACCA
25621881 TAATTCTCCATTT-C-CTTT-TTTTTGGAATTTTATAAAATGATTAAATTCCAGTTTTGGTCCTT
66 TAATTCTCCATTTCCTCTTTATTTTTGGAATTTTATAAAATGATTAAATTCCAGTTTTGGTCCTT
* * *
25621943 TTAACATGCCTAAATTAGAGATTTAATCCATATACTTTATTTTTAACAGAATTTAGTCCCTATTT
131 TTAACATGCCTAAATTAGAGATGTAATCAATATACTTTATTTTTAACAGAATTTAGTCCCCATTT
25622008 TTT
196 TTT
25622011 TTATAATTTT
Statistics
Matches: 184, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
194 106 0.58
195 4 0.02
196 1 0.01
197 15 0.08
198 58 0.32
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.43
Consensus pattern (198 bp):
CAAATCTATACAATCTATATACATATAGTATATATGACCTTCCTGTTAACACGTGTAGACCACCA
TAATTCTCCATTTCCTCTTTATTTTTGGAATTTTATAAAATGATTAAATTCCAGTTTTGGTCCTT
TTAACATGCCTAAATTAGAGATGTAATCAATATACTTTATTTTTAACAGAATTTAGTCCCCATTT
TTT
Found at i:25624324 original size:24 final size:26
Alignment explanation
Indices: 25624272--25624325 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
25624262 TGTTTTTCAA
*
25624272 TTTTCAAAATAAAATATAAAAATTAT
1 TTTTAAAAATAAAATATAAAAATTAT
25624298 TTTTAAAAAT-AAA-ATAAAAA-TAT
1 TTTTAAAAATAAAATATAAAAATTAT
25624321 TTTTA
1 TTTTA
25624326 GTAAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 7 0.26
25 3 0.11
26 9 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (26 bp):
TTTTAAAAATAAAATATAAAAATTAT
Found at i:25624330 original size:26 final size:26
Alignment explanation
Indices: 25624277--25624331 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
25624267 TTCAATTTTC
*
25624277 AAAATAAAATATAAAAATTATTTTTA
1 AAAATAAAATATAAAAATTATTTGTA
25624303 AAAATAAAATA-AAAATATT-TTTAGTA
1 AAAATAAAATATAAAA-ATTATTT-GTA
25624329 AAA
1 AAA
25624332 TTTAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
AAAATAAAATATAAAAATTATTTGTA
Found at i:25626136 original size:2 final size:2
Alignment explanation
Indices: 25626131--25626198 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
25626121 GTGTGTGTAT
25626131 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
25626173 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
25626199 CCTTTATTAG
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:25627528 original size:23 final size:23
Alignment explanation
Indices: 25627502--25627545 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
25627492 AGCATTTTGG
25627502 CACTTTAATGCGATTCATTCTGA
1 CACTTTAATGCGATTCATTCTGA
* *
25627525 CACTTTAGTGGGATTCATTCT
1 CACTTTAATGCGATTCATTCT
25627546 ATGGAGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.16, T:0.41
Consensus pattern (23 bp):
CACTTTAATGCGATTCATTCTGA
Found at i:25627705 original size:25 final size:25
Alignment explanation
Indices: 25627671--25627730 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
25627661 AAAAGTAAAC
*
25627671 AATGACATGTAATTCTGATTTTGAT
1 AATGAAATGTAATTCTGATTTTGAT
* * *
25627696 AATGAAATGTTATTTTGATTTTGGT
1 AATGAAATGTAATTCTGATTTTGAT
*
25627721 AATCAAATGT
1 AATGAAATGT
25627731 CATCTTGAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.17, T:0.45
Consensus pattern (25 bp):
AATGAAATGTAATTCTGATTTTGAT
Found at i:25627738 original size:25 final size:25
Alignment explanation
Indices: 25627686--25627744 Score: 73
Period size: 25 Copynumber: 2.4 Consensus size: 25
25627676 CATGTAATTC
* * *
25627686 TGATTTTGATAATGAAATGTTATTT
1 TGATTTTGATAATCAAATGTCATCT
*
25627711 TGATTTTGGTAATCAAATGTCATCT
1 TGATTTTGATAATCAAATGTCATCT
*
25627736 TGAATTTGA
1 TGATTTTGA
25627745 AAATGATATG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.31, C:0.05, G:0.17, T:0.47
Consensus pattern (25 bp):
TGATTTTGATAATCAAATGTCATCT
Found at i:25630226 original size:19 final size:18
Alignment explanation
Indices: 25630190--25630231 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
25630180 GTGTTTTTCA
25630190 TTATATTCAAATATAATT
1 TTATATTCAAATATAATT
25630208 TATATATTCAAAT-TAAATT
1 T-TATATTCAAATAT-AATT
25630227 TTATA
1 TTATA
25630232 AATAATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.27
19 16 0.73
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATATTCAAATATAATT
Found at i:25630489 original size:52 final size:51
Alignment explanation
Indices: 25630365--25630498 Score: 153
Period size: 52 Copynumber: 2.6 Consensus size: 51
25630355 CTGAACATTA
* * * * * *
25630365 TTTAAAAGCACTTCTCAAAAGTAACACTAAAATCACTTTTTCACGACGCTT
1 TTTAAAAGCACTTCTCAAAAGCAATACTAAAAGCACTTTTTCACAACACCT
** *
25630416 TTTAAAAGCACTTCTTTAAAGCAATACTAAACTAGC-CTTTTTCACAATACCT
1 TTTAAAAGCACTTCTCAAAAGCAATACTAAA--AGCACTTTTTCACAACACCT
*
25630468 TTTAAAAGCATTTCTCAAAAGCAATACTAAA
1 TTTAAAAGCACTTCTCAAAAGCAATACTAAA
25630499 TTAACTCTTA
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
51 27 0.39
52 40 0.58
53 2 0.03
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.32
Consensus pattern (51 bp):
TTTAAAAGCACTTCTCAAAAGCAATACTAAAAGCACTTTTTCACAACACCT
Found at i:25640522 original size:29 final size:29
Alignment explanation
Indices: 25640472--25640677 Score: 145
Period size: 30 Copynumber: 7.0 Consensus size: 29
25640462 TTTTGGACTC
*
25640472 TCGGGGGT-AAAATGATAA-TTTTGGAAGT
1 TCGGAGGTAAAAATG-TAATTTTTGGAAGT
*
25640500 TCGGAGATAAAAATGTAATTTTTGGAAGTT
1 TCGGAGGTAAAAATGTAATTTTTGGAAG-T
* * ** * *
25640530 TAGGGGGTAAAAACATAATTTTTAGAAAT
1 TCGGAGGTAAAAATGTAATTTTTGGAAGT
** *
25640559 T-TTAGGGTCAAAAATATAATTTTTGGAAGT
1 TCGGA-GGT-AAAAATGTAATTTTTGGAAGT
*
25640589 T-TGAGGGTAAAAATGTAATTTTTGGAAGTT
1 TCGGA-GGTAAAAATGTAATTTTTGGAAG-T
* *
25640619 TC-GAGGTCAAAATTGTAATTTTTAGAAGT
1 TCGGAGGT-AAAAATGTAATTTTTGGAAGT
* * *
25640648 TC-AAGGTCAAAATATAATTTTTGGACAGT
1 TCGGAGGTAAAAATGTAATTTTTGGA-AGT
25640677 T
1 T
25640678 TAGAGACTTC
Statistics
Matches: 145, Mismatches: 24, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
28 23 0.16
29 53 0.37
30 69 0.48
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.36
Consensus pattern (29 bp):
TCGGAGGTAAAAATGTAATTTTTGGAAGT
Found at i:25640549 original size:30 final size:30
Alignment explanation
Indices: 25640474--25640680 Score: 153
Period size: 29 Copynumber: 7.0 Consensus size: 30
25640464 TTGGACTCTC
*
25640474 GGGGGT-AAAATGATAA-TTTTGGAAG-TTC
1 GGGGGTAAAAAT-ATAATTTTTGGAAGTTTA
* * *
25640502 GGAGATAAAAATGTAATTTTTGGAAGTTTA
1 GGGGGTAAAAATATAATTTTTGGAAGTTTA
* * *
25640532 GGGGGTAAAAACATAATTTTTAGAAATTTTA
1 GGGGGTAAAAATATAATTTTT-GGAAGTTTA
25640563 --GGGTCAAAAATATAATTTTTGGAAGTTT-
1 GGGGGT-AAAAATATAATTTTTGGAAGTTTA
* *
25640591 GAGGGTAAAAATGTAATTTTTGGAAGTTT-
1 GGGGGTAAAAATATAATTTTTGGAAGTTTA
* * * * * *
25640620 CGAGGTCAAAATTGTAATTTTTAGAAGTTCA
1 GGGGGT-AAAAATATAATTTTTGGAAGTTTA
* *
25640651 --AGGTCAAAATATAATTTTTGGACAGTTTA
1 GGGGGTAAAAATATAATTTTTGGA-AGTTTA
25640680 G
1 G
25640681 AGACTTCCAG
Statistics
Matches: 143, Mismatches: 25, Indels: 20
0.76 0.13 0.11
Matches are distributed among these distances:
28 21 0.15
29 58 0.41
30 57 0.40
31 7 0.05
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (30 bp):
GGGGGTAAAAATATAATTTTTGGAAGTTTA
Found at i:25640627 original size:59 final size:59
Alignment explanation
Indices: 25640476--25640678 Score: 202
Period size: 59 Copynumber: 3.5 Consensus size: 59
25640466 GGACTCTCGG
* *
25640476 GGGT-AAAATGATAA-TTTTGGAAG-TTCGGAGAT-AAAAATGTAATTTTTGGAAGTTTAGG
1 GGGTAAAAAT-ATAATTTTTGGAAGTTTC-GAGGTCAAAAATGTAATTTTTGGAAGTTT-GA
* * * * *
25640534 GGGTAAAAACATAATTTTTAGAAATTT-TAGGGTCAAAAATATAATTTTTGGAAGTTTGA
1 GGGTAAAAATATAATTTTTGGAAGTTTCGA-GGTCAAAAATGTAATTTTTGGAAGTTTGA
* * * *
25640593 GGGTAAAAATGTAATTTTTGGAAGTTTCGAGGTCAAAATTGTAATTTTTAGAAG-TTCA
1 GGGTAAAAATATAATTTTTGGAAGTTTCGAGGTCAAAAATGTAATTTTTGGAAGTTTGA
* *
25640651 AGGTCAAAATATAATTTTTGGACAGTTT
1 GGGTAAAAATATAATTTTTGGA-AGTTT
25640679 AGAGACTTCC
Statistics
Matches: 119, Mismatches: 19, Indels: 13
0.79 0.13 0.09
Matches are distributed among these distances:
58 31 0.26
59 63 0.53
60 25 0.21
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (59 bp):
GGGTAAAAATATAATTTTTGGAAGTTTCGAGGTCAAAAATGTAATTTTTGGAAGTTTGA
Found at i:25642515 original size:6 final size:6
Alignment explanation
Indices: 25642506--25642565 Score: 70
Period size: 6 Copynumber: 10.2 Consensus size: 6
25642496 ACTTTTACTT
* * *
25642506 ATTTAA ATTTATA A--TAA TTTTAA ATTTAA ATGTAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
25642553 ATTTAA ATTTAA A
1 ATTTAA ATTTAA A
25642566 ATAAATAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
4 1 0.02
5 2 0.04
6 40 0.89
7 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:25643023 original size:92 final size:92
Alignment explanation
Indices: 25642909--25643258 Score: 574
Period size: 92 Copynumber: 3.8 Consensus size: 92
25642899 GTTTTTAGTC
* * * *
25642909 CAACTTCAAGAGGATAGGAATTGACGCTTGAAGCTTCATCTTGCTCTTACTACAATTTCAGAGAG
1 CAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAG
* *
25642974 ACAAAAACTTGCTATCCAACTTTACTG
66 ATAAAGACTTGCTATCCAACTTTACTG
*
25643001 CAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTGCTCTTACTACAACTTCAGAGAG
1 CAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAG
* * *
25643066 ATAACGACTTGCTATCAAACTTTATTG
66 ATAAAGACTTGCTATCCAACTTTACTG
* *
25643093 CAACTTCAAGAGGATAGGAATTAATGTTTGAAGCTTCATCTTACTCTTACTACAACTCCAGAGAG
1 CAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAG
25643158 ATAAAGACTTGCTATCCAACTTTACTG
66 ATAAAGACTTGCTATCCAACTTTACTG
* *
25643185 CAACTTTAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTTAGAGAG
1 CAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAG
25643250 ATAAAGACT
66 ATAAAGACT
25643259 CACTATTATA
Statistics
Matches: 240, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
92 240 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (92 bp):
CAACTTCAAGAGGATAGGAATTGATGTTTGAAGCTTCATCTTACTCTTACTACAACTTCAGAGAG
ATAAAGACTTGCTATCCAACTTTACTG
Found at i:25643507 original size:101 final size:101
Alignment explanation
Indices: 25643357--25643940 Score: 706
Period size: 101 Copynumber: 5.8 Consensus size: 101
25643347 AGGTTCATCA
* * * *
25643357 TTGCGACTTAAACATTTCCTTTTTTGTC--TTTGTGGTACTGGAT-TCGCCGTTGCGGTCTTAGA
1 TTGCGACTTAGACCTTTCC-CTTTTGTCTTTTTGCGGTACTGGATCT-GCCGTTGCGGTCTTAGA
* * *
25643419 TCTTTCTCGTCGTGTCTTCTGAGGTACACAGTCCGCTG
64 TCTTTCCCGTCGTGTCTTCTGAGGTACACGGTCCGCCG
* * ** * *
25643457 TTGCAACTTAAACCTTTCCCTTTTGTCTTTTTAAGGTACTGGATCTGCCGTTTCGGTCTTAAATC
1 TTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGATC
* * *
25643522 TTTCTCGTCGTGTCTTTTGAGGTACAGGGTCCGCCG
66 TTTCCCGTCGTGTCTTCTGAGGTACACGGTCCGCCG
* ** * *
25643558 TTACGACTTAGACCTTTTCTTTTTTATCTTTTTTGCGGTACTGGATCTACCGTTGCGGTCTTAGA
1 TTGCGACTTAGACC-TTTCCCTTTTGTC-TTTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGA
** * * *
25643623 TCTTTCCCGTTATGTCTTCTAAGGTACACGGTCCACTG
64 TCTTTCCCGTCGTGTCTTCTGAGGTACACGGTCCGCCG
* * *
25643661 TTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTAGATCTGCCGTTACGGTCTTATATC
1 TTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGATC
* *
25643726 TTTCCCGTCGTGTCTTTTGAGGTACACGATCCGCCG
66 TTTCCCGTCGTGTCTTCTGAGGTACACGGTCCGCCG
* * ** *
25643762 TTGCGACTTAGACCTTTCCCTTTGGTCTTTTTGCGGTACTGGATCCGTGGTTGCGGTCTTAAATC
1 TTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGATC
* *
25643827 TTTCCCGTCGTGTCTTCTAAGGTATACGGTCCGCCG
66 TTTCCCGTCGTGTCTTCTGAGGTACACGGTCCGCCG
* * * * **
25643863 TTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCAGTACTAGATCCGCCTTTGCGACCTTAGATC
1 TTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGATC
*
25643928 TTTCCCATCGTGT
66 TTTCCCGTCGTGT
25643941 TTCATGGTGC
Statistics
Matches: 413, Mismatches: 66, Indels: 9
0.85 0.14 0.02
Matches are distributed among these distances:
99 7 0.02
100 17 0.04
101 294 0.71
102 21 0.05
103 74 0.18
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (101 bp):
TTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGATC
TTTCCCGTCGTGTCTTCTGAGGTACACGGTCCGCCG
Found at i:25643525 original size:51 final size:51
Alignment explanation
Indices: 25643378--25643933 Score: 291
Period size: 51 Copynumber: 11.0 Consensus size: 51
25643368 ACATTTCCTT
* * * *
25643378 TTTTGTC--TTTGTGGTACTGGATTCGCCGTTGCGGTCTTAGATCTTTCTCG
1 TTTTGTCTTTTTGAGGTACTGGATCCGCCGTTGCGGTCTTAGACCTTTC-CC
** * ** * ** *
25643428 TCGTGTC-TTCTGAGGTAC-ACAGTCCGCTGTTGC-AACTTAAACCTTTCCC
1 TTTTGTCTTTTTGAGGTACTGGA-TCCGCCGTTGCGGTCTTAGACCTTTCCC
* * * * * *
25643477 TTTTGTCTTTTTAAGGTACTGGATCTGCCGTTTCGGTCTTAAATCTTTCTCG
1 TTTTGTCTTTTTGAGGTACTGGATCCGCCGTTGCGGTCTTAGACCTTTC-CC
** * * * * **
25643529 TCGTGTC-TTTTGAGGTACAGGGTCCGCCGTTAC-GACTTAGACCTTTTCTT
1 TTTTGTCTTTTTGAGGTACTGGATCCGCCGTTGCGGTCTTAGACC-TTTCCC
* * ** *
25643579 TTTTATCTTTTTTGCGGTACTGGATCTACCGTTGCGGTCTTAGATCTTTCCC
1 TTTTGTC-TTTTTGAGGTACTGGATCCGCCGTTGCGGTCTTAGACCTTTCCC
* * * * * * *
25643631 GTTATGTC-TTCTAAGGTACACGG-TCCACTGTTGC-GACTTAGACCTTTCCC
1 -TTTTGTCTTTTTGAGGTAC-TGGATCCGCCGTTGCGGTCTTAGACCTTTCCC
* * * * * *
25643681 TTTTGTCTTTTTGCGGTACTAGATCTGCCGTTACGGTCTTATATCTTTCCC
1 TTTTGTCTTTTTGAGGTACTGGATCCGCCGTTGCGGTCTTAGACCTTTCCC
** ** *
25643732 GTCGTGTC-TTTTGAGGTACACGATCCGCCGTTGC-GACTTAGACCTTTCCC
1 -TTTTGTCTTTTTGAGGTACTGGATCCGCCGTTGCGGTCTTAGACCTTTCCC
* * ** * *
25643782 TTTGGTCTTTTTGCGGTACTGGATCCGTGGTTGCGGTCTTAAATCTTTCCC
1 TTTTGTCTTTTTGAGGTACTGGATCCGCCGTTGCGGTCTTAGACCTTTCCC
** * * *
25643833 GTCGTGTC-TTCTAAGGTA-TACGG-TCCGCCGTTGC-GACTTAGACCTTTCCC
1 -TTTTGTCTTTTTGAGGTACT--GGATCCGCCGTTGCGGTCTTAGACCTTTCCC
* * ** *
25643883 TTTTGTCTTTTTGCA-GTACTAGATCCGCCTTTGCGACCTTAGATCTTTCCC
1 TTTTGTCTTTTTG-AGGTACTGGATCCGCCGTTGCGGTCTTAGACCTTTCCC
25643934 ATCGTGTTTC
Statistics
Matches: 365, Mismatches: 115, Indels: 51
0.69 0.22 0.10
Matches are distributed among these distances:
49 23 0.06
50 137 0.38
51 149 0.41
52 43 0.12
53 13 0.04
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.40
Consensus pattern (51 bp):
TTTTGTCTTTTTGAGGTACTGGATCCGCCGTTGCGGTCTTAGACCTTTCCC
Found at i:25643740 original size:204 final size:202
Alignment explanation
Indices: 25643385--25643940 Score: 745
Period size: 204 Copynumber: 2.7 Consensus size: 202
25643375 CTTTTTTGTC
* * * *
25643385 TTTGTGGTACTGGAT-TCGCCGTTGCGGTCTTAGATCTTTCTCGTCGTGTCTTCTGAGGTACACA
1 TTTGCGGTACTGGATCT-GCCGTTGCGGTCTTAGATCTTTCCCGTCGTGTCTTCTAAGGTACACG
* * ** * *
25643449 GTCCGCTGTTGCAACTTAAACCTTTCCCTTTTGTCTTTTTAAGGTACTGGATCTGCCGTTTCGGT
65 GTCCGCTGTTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTAGATCTGCCGTTACGGT
* * * **
25643514 CTTAAATCTTTCTCGTCGTGTCTTTTGAGGTACAGGGTCCGCCGTTACGACTTAGACCTTTTCTT
130 CTTAAATCTTTCCCGTCGTGTCTTTTGAGGTACACGATCCGCCGTTACGACTTAGACC-TTTCCC
*
25643579 TTTTATCTTT
194 TTTGATC-TT
* **
25643589 TTTGCGGTACTGGATCTACCGTTGCGGTCTTAGATCTTTCCCGTTATGTCTTCTAAGGTACACGG
1 TTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCGTGTCTTCTAAGGTACACGG
*
25643654 TCCACTGTTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTAGATCTGCCGTTACGGTC
66 TCCGCTGTTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTAGATCTGCCGTTACGGTC
* *
25643719 TTATATCTTTCCCGTCGTGTCTTTTGAGGTACACGATCCGCCGTTGCGACTTAGACCTTTCCCTT
131 TTAAATCTTTCCCGTCGTGTCTTTTGAGGTACACGATCCGCCGTTACGACTTAGACCTTTCCCTT
*
25643784 TGGTCTT
196 TGATCTT
* ** * *
25643791 TTTGCGGTACTGGATCCGTGGTTGCGGTCTTAAATCTTTCCCGTCGTGTCTTCTAAGGTATACGG
1 TTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCGTGTCTTCTAAGGTACACGG
* * * * * **
25643856 TCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCAGTACTAGATCCGCCTTTGCGACC
66 TCCGCTGTTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTAGATCTGCCGTTACGGTC
* *
25643921 TTAGATCTTTCCCATCGTGT
131 TTAAATCTTTCCCGTCGTGT
25643941 TTCATGGTGC
Statistics
Matches: 310, Mismatches: 41, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
202 134 0.43
203 9 0.03
204 166 0.54
205 1 0.00
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.40
Consensus pattern (202 bp):
TTTGCGGTACTGGATCTGCCGTTGCGGTCTTAGATCTTTCCCGTCGTGTCTTCTAAGGTACACGG
TCCGCTGTTGCGACTTAGACCTTTCCCTTTTGTCTTTTTGCGGTACTAGATCTGCCGTTACGGTC
TTAAATCTTTCCCGTCGTGTCTTTTGAGGTACACGATCCGCCGTTACGACTTAGACCTTTCCCTT
TGATCTT
Found at i:25645189 original size:19 final size:18
Alignment explanation
Indices: 25645157--25645197 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
25645147 CTCCTTTCTA
* *
25645157 TTTTTGTTTTTCTTCTTGT
1 TTTTTCTTTCTCTTCTT-T
25645176 TTTTTCTTTCTCTTCTTT
1 TTTTTCTTTCTCTTCTTT
25645194 TTTT
1 TTTT
25645198 ATTTATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.00, C:0.15, G:0.05, T:0.80
Consensus pattern (18 bp):
TTTTTCTTTCTCTTCTTT
Found at i:25653038 original size:28 final size:29
Alignment explanation
Indices: 25653000--25653067 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
25652990 CGGGGTTTGG
25653000 AAATG-TAATTTTTGGA-TACTCG-GGGCA
1 AAATGATAATTTTTGGACT-CTCGAGGGCA
* *
25653027 AGATGATAA-TTTTGGACTCTCGAGGGTA
1 AAATGATAATTTTTGGACTCTCGAGGGCA
25653055 AAATGATAATTTT
1 AAATGATAATTTT
25653068 AGAAGTTCGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 15 0.44
28 16 0.47
29 3 0.09
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (29 bp):
AAATGATAATTTTTGGACTCTCGAGGGCA
Found at i:25653249 original size:29 final size:27
Alignment explanation
Indices: 25653050--25653249 Score: 186
Period size: 29 Copynumber: 7.0 Consensus size: 27
25653040 GGACTCTCGA
* *
25653050 GGGT-AAAATGATAATTTTAGAAGTTCGG
1 GGGTAAAAATG-TAATTTTTGAAGTT-TG
25653078 GGGTAAAAATGTAATTTTTGAAAGTTTCG
1 GGGTAAAAATGTAATTTTTG-AAGTTT-G
* * *
25653107 AGGTGAAAATGGAATTTTTGAAAGTTCTG
1 GGGTAAAAATGTAATTTTTG-AAGTT-TG
25653136 GGGTAAAAATGTAATTTTTGGAAGTTTG
1 GGGTAAAAATGTAATTTTT-GAAGTTTG
* * *
25653164 AGGTTAAAAATATAATTTTTGGAAGTTTAA
1 -GGGTAAAAATGTAATTTTT-GAAGTTT-G
25653194 GGGTAAAAATGTAATTTTTAGAAGTTTG
1 GGGTAAAAATGTAATTTTT-GAAGTTTG
* *
25653222 GGAGTCAAAATATAATTTTTGACAGTTT
1 GG-GTAAAAATGTAATTTTTGA-AGTTT
25653250 AAGGACCTCT
Statistics
Matches: 146, Mismatches: 17, Indels: 17
0.81 0.09 0.09
Matches are distributed among these distances:
28 18 0.12
29 126 0.86
30 2 0.01
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (27 bp):
GGGTAAAAATGTAATTTTTGAAGTTTG
Found at i:25653249 original size:87 final size:86
Alignment explanation
Indices: 25653050--25653249 Score: 219
Period size: 87 Copynumber: 2.3 Consensus size: 86
25653040 GGACTCTCGA
* * * * * *
25653050 GGGT-AAAATGATAATTTTAGAAGTTCGGGGGTAAAAATGTAATTTTTGAAAGTTTCGAGGTGAA
1 GGGTAAAAAT-ATAATTTTTGAAGTTTGAGGGTAAAAATATAATTTTTGAAAGTTTAGAGGTAAA
25653114 AATGGAATTTTTGAAAGTTCTG
65 AATGGAATTTTTGAAAGTTCTG
* * *
25653136 GGGTAAAAATGTAATTTTTGGAAGTTTGAGGTTAAAAATATAATTTTTGGAAGTTTA-AGGGTAA
1 GGGTAAAAATATAATTTTT-GAAGTTTGAGGGTAAAAATATAATTTTTGAAAGTTTAGA-GGTAA
*
25653200 AAATGTAATTTTT-AGAAGTT-TG
64 AAATGGAATTTTTGA-AAGTTCTG
*
25653222 GGAGTCAAAATATAATTTTTGACAGTTT
1 GG-GTAAAAATATAATTTTTGA-AGTTT
25653250 AAGGACCTCT
Statistics
Matches: 96, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
86 19 0.20
87 77 0.80
ACGTcount: A:0.36, C:0.03, G:0.24, T:0.38
Consensus pattern (86 bp):
GGGTAAAAATATAATTTTTGAAGTTTGAGGGTAAAAATATAATTTTTGAAAGTTTAGAGGTAAAA
ATGGAATTTTTGAAAGTTCTG
Found at i:25655068 original size:6 final size:6
Alignment explanation
Indices: 25655059--25655169 Score: 74
Period size: 6 Copynumber: 19.2 Consensus size: 6
25655049 ATTTTTACTT
* * * * *
25655059 ATTTAA ATTT-- ATATAA TTTTAA ATTGAA ATGTAA ATTTAA ACTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
25655105 A-TTAA ATTTAA ATTTTAGA A-ATAA ATTTAA ATTTAA A-ATAA ATTT-A
1 ATTTAA ATTTAA A-TTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
25655151 ATATTAA A-ATAA ATTTAA A
1 AT-TTAA ATTTAA ATTTAA A
25655170 ATGAGTTGAG
Statistics
Matches: 80, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
4 3 0.04
5 18 0.22
6 51 0.64
7 6 0.08
8 2 0.03
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:25655112 original size:17 final size:16
Alignment explanation
Indices: 25655059--25655169 Score: 105
Period size: 17 Copynumber: 6.4 Consensus size: 16
25655049 ATTTTTACTT
* *
25655059 ATTTAAATTTATATAA
1 ATTTAAATTAAAATAA
* *
25655075 TTTTAAATTGAAATGTAA
1 ATTTAAATT-AAA-ATAA
*
25655093 ATTTAAACTTAAATTAA
1 ATTTAAA-TTAAAATAA
25655110 ATTTAAATTTTAGAAATAA
1 ATTTAAA--TTA-AAATAA
25655129 ATTTAAATTTAAAATAA
1 ATTTAAA-TTAAAATAA
25655146 ATTTAATATTAAAATAA
1 ATTTAA-ATTAAAATAA
25655163 ATTTAAA
1 ATTTAAA
25655170 ATGAGTTGAG
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
16 9 0.11
17 38 0.47
18 20 0.25
19 14 0.17
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (16 bp):
ATTTAAATTAAAATAA
Found at i:25656521 original size:28 final size:28
Alignment explanation
Indices: 25656490--25656543 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
25656480 CTTGAAACTG
25656490 TATTAAATTTTA-TTTTTTATTTAATATA
1 TATT-AATTTTATTTTTTTATTTAATATA
**
25656518 TATTTTTTTTATTTTTTTATTTAATA
1 TATTAATTTTATTTTTTTATTTAATA
25656544 AGTCTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (28 bp):
TATTAATTTTATTTTTTTATTTAATATA
Found at i:25657246 original size:29 final size:28
Alignment explanation
Indices: 25657181--25657277 Score: 106
Period size: 29 Copynumber: 3.3 Consensus size: 28
25657171 TTAAATTTTG
*
25657181 GGGTTTATATAAAATTTTCAAAAATTTAAA
1 GGGTTTA-ATAAAATTTTCAAAAAATT-AA
25657211 GGGTTTAAGTAAAATTTTCAAAAAATT-A
1 GGGTTTAA-TAAAATTTTCAAAAAATTAA
* **
25657239 GGAGTTTAATAATAATTTTAAAAAAATCGA
1 GG-GTTTAATAA-AATTTTCAAAAAATTAA
25657269 GGGTTTAAT
1 GGGTTTAAT
25657278 TAATTTTTTA
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
28 6 0.10
29 27 0.45
30 27 0.45
ACGTcount: A:0.45, C:0.03, G:0.14, T:0.37
Consensus pattern (28 bp):
GGGTTTAATAAAATTTTCAAAAAATTAA
Found at i:25657286 original size:29 final size:27
Alignment explanation
Indices: 25657210--25657290 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 27
25657200 AAAAATTTAA
* * *
25657210 AGGGTTTAAGTAAAATTTTCAAAAAATT
1 AGGGTTTAA-TAATATTTTAAAAAAATG
25657238 AGGAGTTTAATAATAATTTTAAAAAAATCG
1 AGG-GTTTAATAAT-ATTTTAAAAAAAT-G
*
25657268 AGGGTTTAATTAATTTTTTAAAA
1 AGGGTTTAA-TAATATTTTAAAA
25657291 GATTTGAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
28 6 0.13
29 32 0.71
30 7 0.16
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (27 bp):
AGGGTTTAATAATATTTTAAAAAAATG
Found at i:25659121 original size:30 final size:29
Alignment explanation
Indices: 25659082--25659156 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
25659072 AAATTTTAAA
*
25659082 TTAATAATAATAAAA-TTACATTGTAATCTT
1 TTAAAAATAATAAAATTTA-ATT-TAATCTT
*
25659112 TTAAAAATAATAAAAATTTAATTTAATTTT
1 TTAAAAATAAT-AAAATTTAATTTAATCTT
25659142 TTAAAAACT-ATAAAA
1 TTAAAAA-TAATAAAA
25659157 ATATAAATTA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
29 4 0.10
30 25 0.62
31 8 0.20
32 3 0.08
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (29 bp):
TTAAAAATAATAAAATTTAATTTAATCTT
Found at i:25660444 original size:20 final size:19
Alignment explanation
Indices: 25660415--25660452 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
25660405 CGTTATAACG
*
25660415 TATATTTATATAACGTATAA
1 TATATGTATATAAC-TATAA
25660435 TATATGTATATAACTATA
1 TATATGTATATAACTATA
25660453 TTACATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
TATATGTATATAACTATAA
Found at i:25685937 original size:6 final size:6
Alignment explanation
Indices: 25685913--25685970 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
25685903 CAATCAAATC
*
25685913 ATTTAAA ATTT-A TTTTAA ATTTAA ATTT-- ATTTAA ATTTAA ATTT-A
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
25685958 ATATAA ATTTAA A
1 ATTTAA ATTTAA A
25685971 ATTATTATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
4 4 0.09
5 8 0.19
6 27 0.63
7 4 0.09
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATTTAA
Found at i:25685940 original size:17 final size:17
Alignment explanation
Indices: 25685913--25685986 Score: 105
Period size: 17 Copynumber: 4.4 Consensus size: 17
25685903 CAATCAAATC
*
25685913 ATTTAAAATTTATTTTAA
1 ATTT-AAATTTATTATAA
25685931 ATTTAAATTTATT-TAA
1 ATTTAAATTTATTATAA
*
25685947 ATTTAAATTTAATATAA
1 ATTTAAATTTATTATAA
*
25685964 ATTTAAAATTATTATAA
1 ATTTAAATTTATTATAA
25685981 ATTTAA
1 ATTTAA
25685987 TTAAATGAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.29
17 33 0.63
18 4 0.08
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTATTATAA
Found at i:25686699 original size:21 final size:21
Alignment explanation
Indices: 25686675--25686714 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
25686665 CATTAAATAA
*
25686675 TTTAATAAATATTAATAATGT
1 TTTAATAAAAATTAATAATGT
25686696 TTTAATAAAAATTAATAAT
1 TTTAATAAAAATTAATAAT
25686715 AATAATAATA
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:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TTTAATAAAAATTAATAATGT
Found at i:25686716 original size:3 final size:3
Alignment explanation
Indices: 25686698--25686731 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
25686688 AATAATGTTT
*
25686698 TAA TAA AAA TTAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA
25686732 GAAGGCAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:25687867 original size:30 final size:30
Alignment explanation
Indices: 25687833--25688040 Score: 191
Period size: 30 Copynumber: 6.9 Consensus size: 30
25687823 GAAAGTCCTT
* * *
25687833 AAACTTTTCCAAAATTACATTTTGACCCCC
1 AAACTTTTTCAAAATTACATTTTAACCCCA
* * ** *
25687863 AAACTATTCCAAAATTATTTTTTAACCCTA
1 AAACTTTTTCAAAATTACATTTTAACCCCA
* * **
25687893 AAACTTTTTGAAAATTATATTTTAACCTTA
1 AAACTTTTTCAAAATTACATTTTAACCCCA
** * **
25687923 AAACTTTTTGTAAATTACATTTTGACCCTT
1 AAACTTTTTCAAAATTACATTTTAACCCCA
* * *
25687953 AAACTTTTTTAAAATTCCATTTTTACCCCA
1 AAACTTTTTCAAAATTACATTTTAACCCCA
* *
25687983 AAACTTTTTAAAAATTACATTTTAACCCCC
1 AAACTTTTTCAAAATTACATTTTAACCCCA
* *
25688013 AAACTTTTACAAAATTCCATTTTTAACC
1 AAACTTTTTCAAAATTACA-TTTTAACC
25688041 TCAATTTCAC
Statistics
Matches: 148, Mismatches: 29, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
30 140 0.95
31 8 0.05
ACGTcount: A:0.37, C:0.21, G:0.02, T:0.41
Consensus pattern (30 bp):
AAACTTTTTCAAAATTACATTTTAACCCCA
Found at i:25688028 original size:90 final size:90
Alignment explanation
Indices: 25687833--25688035 Score: 230
Period size: 90 Copynumber: 2.3 Consensus size: 90
25687823 GAAAGTCCTT
* *
25687833 AAACTTTTCCAAAATTACATTTTGACCCCCAAACTATTCCAAAATTATTTTTTAACCCTAAAACT
1 AAACTTTTACAAAATTACATTTTGACCCCCAAACTATTCCAAAATTATTTTTTAACCCCAAAACT
* * **
25687898 TTTTGAAAATTATATTTTAACCTTA
66 TTTTAAAAATTACATTTTAACCCCA
*** ** * **
25687923 AAACTTTTTGTAAATTACATTTTGACCCTTAAACTTTTTTAAAATTCCA-TTTTT-ACCCCAAAA
1 AAACTTTTACAAAATTACATTTTGACCCCCAAACTATTCCAAAATT--ATTTTTTAACCCCAAAA
*
25687986 CTTTTTAAAAATTACATTTTAACCCCC
64 CTTTTTAAAAATTACATTTTAACCCCA
*
25688013 AAACTTTTACAAAATTCCATTTT
1 AAACTTTTACAAAATTACATTTT
25688036 TAACCTCAAT
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
90 87 0.94
91 5 0.05
92 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.02, T:0.41
Consensus pattern (90 bp):
AAACTTTTACAAAATTACATTTTGACCCCCAAACTATTCCAAAATTATTTTTTAACCCCAAAACT
TTTTAAAAATTACATTTTAACCCCA
Found at i:25688057 original size:30 final size:30
Alignment explanation
Indices: 25688023--25688167 Score: 97
Period size: 30 Copynumber: 4.9 Consensus size: 30
25688013 AAACTTTTAC
25688023 AAAATTCCATTTTTAACCTCAATTTCACTA
1 AAAATTCCATTTTTAACCTCAATTTCACTA
* *
25688053 AAAATTACCA-TTTTACCCTCGAACTTT-TC-A
1 AAAATT-CCATTTTTAACCTC-AA-TTTCACTA
* * * *
25688083 AAAATCCCATTTTTGACCTCGATTTCACCA
1 AAAATTCCATTTTTAACCTCAATTTCACTA
* *
25688113 AAAATTACCA-TTTTACCCTCGAACTT--CTA
1 AAAATT-CCATTTTTAACCTC-AATTTCACTA
* * *
25688142 AAAATCCCGTTTTTGACCT-AATTTCA
1 AAAATTCCATTTTTAACCTCAATTTCA
25688168 ACCAAAATTA
Statistics
Matches: 86, Mismatches: 18, Indels: 23
0.68 0.14 0.18
Matches are distributed among these distances:
27 4 0.05
28 5 0.06
29 19 0.22
30 43 0.50
31 12 0.14
32 3 0.03
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (30 bp):
AAAATTCCATTTTTAACCTCAATTTCACTA
Found at i:25688064 original size:31 final size:30
Alignment explanation
Indices: 25688023--25688126 Score: 99
Period size: 30 Copynumber: 3.5 Consensus size: 30
25688013 AAACTTTTAC
25688023 AAAATT-CCATTTTTAACCTCAATTTCACTA
1 AAAATTACCATTTTTAACCTCAATTTCAC-A
* *
25688053 AAAATTACCA-TTTTACCCTCGAACTTT-TCA
1 AAAATTACCATTTTTAACCTC-AA-TTTCACA
* * *
25688083 AAAA-TCCCATTTTTGACCTCGATTTCACCA
1 AAAATTACCATTTTTAACCTCAATTTCA-CA
25688113 AAAATTACCATTTT
1 AAAATTACCATTTT
25688127 ACCCTCGAAC
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
28 3 0.05
29 5 0.08
30 34 0.58
31 14 0.24
32 3 0.05
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.38
Consensus pattern (30 bp):
AAAATTACCATTTTTAACCTCAATTTCACA
Found at i:25688174 original size:59 final size:59
Alignment explanation
Indices: 25687992--25688191 Score: 253
Period size: 60 Copynumber: 3.4 Consensus size: 59
25687982 AAAACTTTTT
* * * * *
25687992 AAAAATTA-CATTTTAACCCCCAAACTTTTACAAAATTCCATTTTTAACCTCAATTTCACT
1 AAAAATTACCATTTT-ACCCTCGAACTTTTA-AAAATCCCATTTTTGACCTCAATTTCACC
*
25688052 AAAAATTACCATTTTACCCTCGAACTTTTCAAAAATCCCATTTTTGACCTCGATTTCACC
1 AAAAATTACCATTTTACCCTCGAACTTTT-AAAAATCCCATTTTTGACCTCAATTTCACC
* *
25688112 AAAAATTACCATTTTACCCTCGAACTTCTAAAAATCCCGTTTTTGACCT-AATTTCAACC
1 AAAAATTACCATTTTACCCTCGAACTTTTAAAAATCCCATTTTTGACCTCAATTTC-ACC
* *
25688171 -AAAATTACCGTTTTGCCCTCG
1 AAAAATTACCATTTTACCCTCG
25688192 GGTATCCAAA
Statistics
Matches: 126, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
58 24 0.19
59 22 0.17
60 73 0.58
61 7 0.06
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (59 bp):
AAAAATTACCATTTTACCCTCGAACTTTTAAAAATCCCATTTTTGACCTCAATTTCACC
Found at i:25698072 original size:92 final size:92
Alignment explanation
Indices: 25697947--25698862 Score: 1501
Period size: 92 Copynumber: 10.0 Consensus size: 92
25697937 AGATCAAAAT
*
25697947 AACATCAATTCTTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
*
25698012 TTGTAGTAAGAGCTAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* *
25698039 AACATCAAATCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
*
25698104 TTGTAGTAAGAGCAAGATAAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* * *
25698131 AACATCAATTCCTATCCTCTTAAAGTTGTAGTAAAGTTGGGTAGCAAGTCTTTGTCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
*
25698196 TTGTAGTAAGAGCAAGATGAAGCGTCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* * *
25698223 AACATTAATTCCTATCATCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTATCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
25698288 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* * * * *
25698315 AACATCAATTCCTATCCTTTTGAAGTTGTAGTAAAGTTGGGTAGTAAGGCTTTGTCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
*
25698380 TTGTAGTAAGAGCAAGATGAAGCGTCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
*
25698407 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
25698472 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
*
25698499 AACATCAATTCCTATCATCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
25698564 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
*
25698591 AACATCAGTTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
* * * *
25698656 TTGAAGTAAGAACAAGACGAAGCATCG
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* * *
25698683 AACATTAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTATCTCTCCGAAG
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
25698748 TTGTAGTAAGAGCAAGATGAAGCATCA
66 TTGTAGTAAGAGCAAGATGAAGCATCA
* * * * * *
25698775 AACGTCAATTCTTATCCTCTTGAAGTTATAGTAAAGTTGGATAACGAA-TCTTTATCTCTCTGAA
1 AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGC-AAGTCTTTGTCTCTCTGAA
*
25698839 GTTGTAGTAAGAGCATGATGAAGC
65 GTTGTAGTAAGAGCAAGATGAAGC
25698863 TTAGACGTCA
Statistics
Matches: 766, Mismatches: 57, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
92 764 1.00
93 2 0.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (92 bp):
AACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGATGGATAGCAAGTCTTTGTCTCTCTGAAG
TTGTAGTAAGAGCAAGATGAAGCATCA
Found at i:25699142 original size:17 final size:17
Alignment explanation
Indices: 25699115--25699206 Score: 121
Period size: 17 Copynumber: 5.4 Consensus size: 17
25699105 CAATCAAATC
25699115 ATTTAAAATTTATTTTAA
1 ATTT-AAATTTATTTTAA
*
25699133 AATTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
25699150 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* * *
25699167 ATTTAGATTTAATATAA
1 ATTTAAATTTATTTTAA
* *
25699184 ATTTAAAATTATTATAA
1 ATTTAAATTTATTTTAA
25699201 ATTTAA
1 ATTTAA
25699207 TTAAATAAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
17 63 0.95
18 3 0.05
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:25699917 original size:9 final size:9
Alignment explanation
Indices: 25699856--25699944 Score: 53
Period size: 9 Copynumber: 9.9 Consensus size: 9
25699846 ATGATAATGA
25699856 TAATAATAT
1 TAATAATAT
*
25699865 CAATAATA-
1 TAATAATAT
*
25699873 AAATAATAT
1 TAATAATAT
**
25699882 TAA-AGGCAT
1 TAATA-ATAT
25699891 TAAATAAT-T
1 T-AATAATAT
25699900 TAATAAATAT
1 TAAT-AATAT
25699910 TAATAATATTT
1 TAATAATA--T
25699921 TAATAA-A-
1 TAATAATAT
*
25699928 TAATAATAA
1 TAATAATAT
25699937 TAATAATA
1 TAATAATA
25699945 AGGCAAAGGG
Statistics
Matches: 63, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
7 6 0.10
8 12 0.19
9 29 0.46
10 8 0.13
11 8 0.13
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (9 bp):
TAATAATAT
Found at i:25699917 original size:21 final size:21
Alignment explanation
Indices: 25699893--25699940 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
25699883 AAAGGCATTA
*
25699893 AATAATTTAATAAATATTAAT
1 AATAATTTAATAAATAATAAT
*
25699914 AATATTTTAATAAATAATAAT
1 AATAATTTAATAAATAATAAT
25699935 AATAAT
1 AATAAT
25699941 AATAAGGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AATAATTTAATAAATAATAAT
Found at i:25701073 original size:30 final size:30
Alignment explanation
Indices: 25701032--25701229 Score: 238
Period size: 30 Copynumber: 6.7 Consensus size: 30
25701022 CCTTGGAAGT
* *
25701032 CCCTGAACTTTTCCAAAATTATATTTTGAC
1 CCCTAAACTTTTTCAAAATTATATTTTGAC
25701062 CCCTAAACTTTTTCAAAATTATATTTTGAC
1 CCCTAAACTTTTTCAAAATTATATTTTGAC
* * * *
25701092 CCCAAAACTTTTTGAAACTTATA-TTTAAC
1 CCCTAAACTTTTTCAAAATTATATTTTGAC
* ** *
25701121 CCCAAAACTTTTTGTAAATTACATTTTGAC
1 CCCTAAACTTTTTCAAAATTATATTTTGAC
* *
25701151 CCTTAAACTTTTTCGAAATTATATTTTGAC
1 CCCTAAACTTTTTCAAAATTATATTTTGAC
* * * *
25701181 CCCAAAACTTTCTAAAAATTACATTTTGAC
1 CCCTAAACTTTTTCAAAATTATATTTTGAC
25701211 CCCTAAACTTTTT-AAAATT
1 CCCTAAACTTTTTCAAAATT
25701230 CCATTTTTAC
Statistics
Matches: 144, Mismatches: 23, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
29 31 0.22
30 113 0.78
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (30 bp):
CCCTAAACTTTTTCAAAATTATATTTTGAC
Found at i:25701140 original size:89 final size:90
Alignment explanation
Indices: 25701047--25701236 Score: 267
Period size: 89 Copynumber: 2.1 Consensus size: 90
25701037 AACTTTTCCA
* * * *
25701047 AAATTATATTTTGACCCCTAAACTTTTTCAAAATTATATTTTGACCCCAAAACTTTTTGAAACTT
1 AAATTACATTTTGACCCCTAAACTTTTTCAAAATTATATTTTGACCCCAAAACTTTCTAAAAATT
*
25701112 ATA-TTTAACCCCAAAACTTTTTGT
66 ACATTTTAACCCCAAAACTTTTTGT
* *
25701136 AAATTACATTTTGACCCTTAAACTTTTTCGAAATTATATTTTGACCCCAAAACTTTCTAAAAATT
1 AAATTACATTTTGACCCCTAAACTTTTTCAAAATTATATTTTGACCCCAAAACTTTCTAAAAATT
* * *
25701201 ACATTTTGACCCCTAAACTTTTT-A
66 ACATTTTAACCCCAAAACTTTTTGT
*
25701225 AAATTCCATTTT
1 AAATTACATTTT
25701237 TACGCCCGAT
Statistics
Matches: 89, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
89 72 0.81
90 17 0.19
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (90 bp):
AAATTACATTTTGACCCCTAAACTTTTTCAAAATTATATTTTGACCCCAAAACTTTCTAAAAATT
ACATTTTAACCCCAAAACTTTTTGT
Found at i:25701287 original size:59 final size:58
Alignment explanation
Indices: 25701224--25701442 Score: 255
Period size: 59 Copynumber: 3.7 Consensus size: 58
25701214 TAAACTTTTT
25701224 AAAATTCCATTTTTACGCCCGATTTCACC-AAAATTACCATTTTACCCTCGAACTCTCCA
1 AAAATTCCATTTTTAC-CCCGATTTCACCAAAAATTACCATTTTACCCTCGAACT-TCCA
* * * * *
25701283 AAAATTCCATTTTTGACCTCGATTTCACCAAAAATTATCATTTTACCCCCAAACTTTTCA
1 AAAATTCCATTTTT-ACCCCGATTTCACCAAAAATTACCATTTTACCCTCGAAC-TTCCA
* * * * *
25701343 AAAATACCATTTTAACCCCGATTTCACCAAAAATTATCATTTTACTCTCGAACTTCTA
1 AAAATTCCATTTTTACCCCGATTTCACCAAAAATTACCATTTTACCCTCGAACTTCCA
* *
25701401 AAAATCCCATTTTTTA-CCCAATTTCAACC-AAAATTACCATTT
1 AAAATTCCA-TTTTTACCCCGATTTC-ACCAAAAATTACCATTT
25701443 CGCCCCCGAG
Statistics
Matches: 138, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
58 31 0.22
59 68 0.49
60 38 0.28
61 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAATTCCATTTTTACCCCGATTTCACCAAAAATTACCATTTTACCCTCGAACTTCCA
Found at i:25701386 original size:30 final size:30
Alignment explanation
Indices: 25701224--25701386 Score: 133
Period size: 30 Copynumber: 5.5 Consensus size: 30
25701214 TAAACTTTTT
*
25701224 AAAATT-CCATTTTTACGCCCGATTTCACC-
1 AAAATTACCATTTTAAC-CCCGATTTCACCA
** *
25701253 AAAATTACCATTTT-ACCCTCGAACTCTCCA
1 AAAATTACCATTTTAACCC-CGATTTCACCA
* *
25701283 AAAATT-CCATTTTTGACCTCGATTTCACCA
1 AAAATTACCA-TTTTAACCCCGATTTCACCA
* * * *
25701313 AAAATTATCATTTTACCCCCAAACTTT--TCA
1 AAAATTACCATTTTAACCCC-GA-TTTCACCA
25701343 AAAA-TACCATTTTAACCCCGATTTCACCA
1 AAAATTACCATTTTAACCCCGATTTCACCA
*
25701372 AAAATTATCATTTTA
1 AAAATTACCATTTTA
25701387 CTCTCGAACT
Statistics
Matches: 105, Mismatches: 18, Indels: 21
0.73 0.12 0.15
Matches are distributed among these distances:
27 3 0.03
28 3 0.03
29 37 0.35
30 53 0.50
31 6 0.06
32 3 0.03
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTACCATTTTAACCCCGATTTCACCA
Found at i:25702448 original size:9 final size:8
Alignment explanation
Indices: 25702433--25702476 Score: 52
Period size: 9 Copynumber: 5.2 Consensus size: 8
25702423 ATGTTTGAAA
25702433 TTTTTTAT
1 TTTTTTAT
25702441 TATTTTTAT
1 T-TTTTTAT
* *
25702450 TTTTTAAA
1 TTTTTTAT
25702458 TTTTTTAT
1 TTTTTTAT
25702466 TATTTTTAT
1 T-TTTTTAT
25702475 TT
1 TT
25702477 GCTTAATTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
8 14 0.47
9 16 0.53
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTAT
Found at i:25702475 original size:25 final size:25
Alignment explanation
Indices: 25702420--25702476 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
25702410 TTTGAAAAAA
*
25702420 TTTATGTTTGAAATTTTTTATTATT
1 TTTATTTTTGAAATTTTTTATTATT
*
25702445 TTTATTTTTTAAATTTTTTATTATT
1 TTTATTTTTGAAATTTTTTATTATT
25702470 TTTATTT
1 TTTATTT
25702477 GCTTAATTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (25 bp):
TTTATTTTTGAAATTTTTTATTATT
Found at i:25702484 original size:25 final size:25
Alignment explanation
Indices: 25702430--25702482 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
25702420 TTTATGTTTG
*
25702430 AAATTTTTTATTATTTTTATTTTTT
1 AAATTTTTTATTATTTTTATTTCTT
25702455 AAATTTTTTATTATTTTTATTTGCTT
1 AAATTTTTTATTATTTTTATTT-CTT
25702481 AA
1 AA
25702483 TTGAGAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (25 bp):
AAATTTTTTATTATTTTTATTTCTT
Found at i:25704734 original size:4 final size:4
Alignment explanation
Indices: 25704725--25704749 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
25704715 TAAAAACAAC
25704725 AATT AATT AATT AATT AATT AATT A
1 AATT AATT AATT AATT AATT AATT A
25704750 GTGGAATTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:25711296 original size:17 final size:18
Alignment explanation
Indices: 25711256--25711297 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
25711246 TGTAAAATCA
25711256 AATAAAATTATATTTAAT
1 AATAAAATTATATTTAAT
* * *
25711274 ATTAAATTTAT-TTTATT
1 AATAAAATTATATTTAAT
25711291 AATAAAA
1 AATAAAA
25711298 CTATGAAATA
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
AATAAAATTATATTTAAT
Found at i:25713925 original size:2 final size:2
Alignment explanation
Indices: 25713918--25713943 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
25713908 ATATTTTCTA
25713918 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
25713944 GTTTGTTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25719344 original size:62 final size:62
Alignment explanation
Indices: 25719232--25719406 Score: 221
Period size: 62 Copynumber: 2.8 Consensus size: 62
25719222 TTTCAAATTT
* *
25719232 TTTGGGAATTTAGGGATTTAAGTTTTAAAATTTTAGGGATTTTCGGGATTTTT-AGGGTTGTTGG
1 TTTGGGAATTT-TGG-TTTAAG-TTTAAAAATTTAGGGATTTTCGGGATTTTTGA-GGTTGTTGG
25719296 G
62 G
* *
25719297 TTTGGGGAA-TTTGGTTTAGGTTTAAAAAATTTGGGGATTTT-GGGATTTTTGAGGTTGTTGGG
1 TTT-GGGAATTTTGGTTTAAGTTT-AAAAATTTAGGGATTTTCGGGATTTTTGAGGTTGTTGGG
* *
25719359 TTTGGGAATTTTGGTTTAAGTTTAAAAATTTCGAGATTTTCGGGATTT
1 TTTGGGAATTTTGGTTTAAGTTTAAAAATTTAGGGATTTTCGGGATTT
25719407 AGATTTTAAA
Statistics
Matches: 98, Mismatches: 7, Indels: 13
0.83 0.06 0.11
Matches are distributed among these distances:
61 20 0.20
62 45 0.46
63 21 0.21
64 2 0.02
65 5 0.05
66 5 0.05
ACGTcount: A:0.22, C:0.02, G:0.30, T:0.46
Consensus pattern (62 bp):
TTTGGGAATTTTGGTTTAAGTTTAAAAATTTAGGGATTTTCGGGATTTTTGAGGTTGTTGGG
Found at i:25720555 original size:17 final size:16
Alignment explanation
Indices: 25720533--25720575 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
25720523 TATTTTATTG
25720533 TTTTTTACTTTAATTT
1 TTTTTTACTTTAATTT
*
25720549 ATTTTTTAAATTTAATTT
1 -TTTTTT-ACTTTAATTT
25720567 TTTTTTACT
1 TTTTTTACT
25720576 GACGTGGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 12 0.52
18 9 0.39
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTTTACTTTAATTT
Found at i:25729626 original size:2 final size:2
Alignment explanation
Indices: 25729619--25729656 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
25729609 GATTTCACTT
25729619 TC TC TC TC T- TC TC TC 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 TC TC TC TC T
25729657 TCTATATCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:25742326 original size:20 final size:18
Alignment explanation
Indices: 25742280--25742327 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
25742270 TATGTAATTG
*
25742280 TATTTTTTTAATAAGAGT
1 TATTTTTTTAATAAAAGT
25742298 TATTGTTTTTTAAAATAAAAGT
1 TA-T-TTTTTT--AATAAAAGT
25742320 TATTTTTT
1 TATTTTTT
25742328 ATTTTTAGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 2 0.08
19 1 0.04
20 11 0.44
21 1 0.04
22 10 0.40
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
TATTTTTTTAATAAAAGT
Found at i:25743997 original size:29 final size:30
Alignment explanation
Indices: 25743966--25744188 Score: 185
Period size: 29 Copynumber: 7.5 Consensus size: 30
25743956 GTTTGGGGGT
25743966 AAAATGGTAATTTTGGTAAAATCAGGGTTA
1 AAAATGGTAATTTTGGTAAAATCAGGGTTA
* * *
25743996 AAAATGG-GATTTTGGGAAATTCGAGGG-T-
1 AAAATGGTAATTTTGGTAAAATC-AGGGTTA
* * *
25744024 AAAATGGTAATTTTGGTGAAACCAAGGTTA
1 AAAATGGTAATTTTGGTAAAATCAGGGTTA
* *
25744054 AAAAT-G-AGATTTTGGGAAAATTCAGGGGT-
1 AAAATGGTA-ATTTTGGTAAAA-TCAGGGTTA
*
25744083 AAAATGGTAATTTTGGTGAAATCAGGGTTA
1 AAAATGGTAATTTTGGTAAAATCAGGGTTA
* * * *
25744113 AAAATGG-GATTTTGGAAAAATTTAGGGGT-
1 AAAATGGTAATTTTGGTAAAA-TCAGGGTTA
* *
25744142 AAAATGGTAATTTTTTGGTGAAATCGGGGTTA
1 AAAATGGTAA--TTTTGGTAAAATCAGGGTTA
*
25744174 AAAATGG-GATTTTGG
1 AAAATGGTAATTTTGG
25744189 AAAGTTTGGG
Statistics
Matches: 150, Mismatches: 29, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
28 11 0.07
29 70 0.47
30 46 0.31
31 7 0.05
32 16 0.11
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTGGTAAAATCAGGGTTA
Found at i:25744217 original size:30 final size:30
Alignment explanation
Indices: 25744122--25744278 Score: 96
Period size: 29 Copynumber: 5.2 Consensus size: 30
25744112 AAAAATGGGA
* *
25744122 TTTTGGAAAAATTTAGGGGTAAAATGGTAATT
1 TTTTGG-AAAGTTTGGGGGTAAAATGGTAA-T
* * *
25744154 TTTTGGTGAAA--TCGGGGTTAAAAATGG-GA-
1 TTTT-G-GAAAGTTTGGGGGT-AAAATGGTAAT
* *
25744183 TTTTGGAAAGTTTGGGGGTAAAACGATAAT
1 TTTTGGAAAGTTTGGGGGTAAAATGGTAAT
* *
25744213 TTTTGGTGAAA--TCGGGGTTGAAAATGGT-A-
1 TTTT-G-GAAAGTTTGGGGGT-AAAATGGTAAT
*
25744242 TTTTGAAAAGTTTGGGGGTAAAATGGTAAT
1 TTTTGGAAAGTTTGGGGGTAAAATGGTAAT
25744272 TTTTGGA
1 TTTTGGA
25744279 CAGTCCAGGG
Statistics
Matches: 94, Mismatches: 17, Indels: 30
0.67 0.12 0.21
Matches are distributed among these distances:
27 7 0.07
28 15 0.16
29 22 0.23
30 17 0.18
31 13 0.14
32 15 0.16
33 4 0.04
34 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.36
Consensus pattern (30 bp):
TTTTGGAAAGTTTGGGGGTAAAATGGTAAT
Found at i:25744245 original size:29 final size:29
Alignment explanation
Indices: 25743960--25744246 Score: 168
Period size: 29 Copynumber: 9.7 Consensus size: 29
25743950 CAAAAAGTTT
* *
25743960 GGGGGTAAAATGGTAATTTTGGTAAAATC
1 GGGGTTAAAATGGTAATTTTGGTGAAATC
* *
25743989 AGGGTTAAAAATGG-GATTTTGG-GAAATTC
1 GGGGTT-AAAATGGTAATTTTGGTGAAA-TC
*
25744018 GAGGG-TAAAATGGTAATTTTGGTGAAACC
1 G-GGGTTAAAATGGTAATTTTGGTGAAATC
**
25744047 AAGGTTAAAAAT-G-AGATTTTGG-GAAAATTC
1 GGGGTT-AAAATGGTA-ATTTTGGTG-AAA-TC
25744077 AGGGG-TAAAATGGTAATTTTGGTGAAATC
1 -GGGGTTAAAATGGTAATTTTGGTGAAATC
* * ** *
25744106 AGGGTTAAAAATGG-GATTTTGGAAAAATTTA
1 GGGGTT-AAAATGGTAATTTTGGTGAAA--TC
25744137 GGGG-TAAAATGGTAATTTTTTGGTGAAATC
1 GGGGTTAAAATGGTAA--TTTTGGTGAAATC
* *
25744167 GGGGTTAAAAATGG-GATTTT-G-GAAAGTTT
1 GGGGTT-AAAATGGTAATTTTGGTGAAA--TC
* * *
25744196 GGGGGTAAAACGATAATTTTTGGTGAAATC
1 GGGGTTAAAATGGTAA-TTTTGGTGAAATC
25744226 GGGGTTGAAAATGGT-ATTTTG
1 GGGGTT-AAAATGGTAATTTTG
25744247 AAAAGTTTGG
Statistics
Matches: 196, Mismatches: 32, Indels: 60
0.68 0.11 0.21
Matches are distributed among these distances:
27 4 0.02
28 23 0.12
29 75 0.38
30 57 0.29
31 17 0.09
32 20 0.10
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.32
Consensus pattern (29 bp):
GGGGTTAAAATGGTAATTTTGGTGAAATC
Found at i:25744275 original size:59 final size:60
Alignment explanation
Indices: 25743908--25744277 Score: 452
Period size: 59 Copynumber: 6.3 Consensus size: 60
25743898 CCGACGGTAC
** * * **
25743908 AAAAT-GTAATTTTACGTGAAATTAGGGTTAAAAAT-GGAATTTCAAAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAAGTTTGGGGGT
* * * *
25743966 AAAATGGTAA-TTTTGGTAAAATCAGGGTTAAAAATGGGATTTTGGGAAA-TTCGAGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAAGTTTGGGGGT
* * * **
25744024 AAAATGGTAA-TTTTGGTGAAACCAAGGTTAAAAATGAGATTTTGGGAAAA-TTCAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTT-GGAAAAGTTTGGGGGT
* *
25744083 AAAATGGTAA-TTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAAATTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAAGTTTGGGGGT
*
25744142 AAAATGGTAATTTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGG-AAAGTTTGGGGGT
1 AAAATGGTAA-TTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAAGTTTGGGGGT
* * * * *
25744202 AAAACGATAATTTTTGGTGAAATCGGGGTTGAAAATGGTATTTT-GAAAAGTTTGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAAGTTTGGGGGT
25744261 AAAATGGTAATTTTTGG
1 AAAATGGTAATTTTTGG
25744278 ACAGTCCAGG
Statistics
Matches: 275, Mismatches: 30, Indels: 13
0.86 0.09 0.04
Matches are distributed among these distances:
58 79 0.29
59 143 0.52
60 19 0.07
61 34 0.12
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.33
Consensus pattern (60 bp):
AAAATGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGGATTTTGGAAAAGTTTGGGGGT
Found at i:25746215 original size:17 final size:15
Alignment explanation
Indices: 25746165--25746219 Score: 53
Period size: 17 Copynumber: 3.6 Consensus size: 15
25746155 ATGGAAATTT
25746165 AATTT-AATTT-T-A
1 AATTTAAATTTATAA
25746177 AATTTAAATTTATAA
1 AATTTAAATTTATAA
25746192 TAGATTTAAATTGTATACA
1 -A-ATTTAAATT-TATA-A
25746211 AATTTAAAT
1 AATTTAAAT
25746220 CCAAAATAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
12 5 0.14
13 5 0.14
14 1 0.03
15 1 0.03
16 1 0.03
17 17 0.47
18 5 0.14
19 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (15 bp):
AATTTAAATTTATAA
Found at i:25747013 original size:201 final size:201
Alignment explanation
Indices: 25746552--25747183 Score: 930
Period size: 201 Copynumber: 3.2 Consensus size: 201
25746542 TTCTTCTTTG
* * * *
25746552 TCTCATCAGGAAGATGACCGCAAT-TC-TGTTTTAATTCGCTTCTCTGGATCTCCTCAGGAAGAC
1 TCTCATCAGGAAGATGACCGC-CTCGCTTGTTTTGATTCGCTTCTCTGGATCTCTTCAGGAAGAC
* * *
25746615 AAATTTGGTCCACTTCTCTGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTCGTCCTGCTTCT
65 GAATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGTCCTGCTTCT
* * *
25746680 CAGTGTCTCATCAGAAAGCTGGG-TCGAAGATTTGCTCAAGTCTGAGCGTTGAA-TTGGTATTCT
130 CAGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGAGTTTGAGCGTT-AAGTTGGTATTCT
25746743 TCTCTGTA
194 TCTCTGTA
* * * *
25746751 TCTCATTAGGAAGATGACCTCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTTTTCAGGAAGATG
1 TCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTCTTCAGGAAGACG
*
25746816 AATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTACTGCTTCGTCCTGCTTCTC
66 AATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGTCCTGCTTCTC
* * * *
25746881 AGTATCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGTGTTTGAGCGCTAAGTTGGTGTTCTTC
131 AGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGAGTTTGAGCGTTAAGTTGGTATTCTTC
25746946 TCTGTA
196 TCTGTA
*
25746952 TCTCATCAGGAAGATGACCTCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTCTTCAGGAAGACG
1 TCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTCTTCAGGAAGACG
* ** * *
25747017 AATCTGGTCCACTTCTCTATATCTCATCAGGAAGCTAACCCATTTATTGCTTCGACTTGCTTCTC
66 AATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGTCCTGCTTCTC
* * * *
25747082 TGTGTCTCATCAGGAAGCCGTGTTCGAAGATTTGCTCGAGTTTGAGCGTTGAGTTGGTATTCTTC
131 AGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGAGTTTGAGCGTTAAGTTGGTATTCTTC
25747147 TCTGTA
196 TCTGTA
* * *
25747153 TCTCATCAGGGAGATGATCGCCTCACTTGTT
1 TCTCATCAGGAAGATGACCGCCTCGCTTGTT
25747184 GAACTACTCC
Statistics
Matches: 389, Mismatches: 40, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
198 1 0.00
199 20 0.05
200 117 0.30
201 251 0.65
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.36
Consensus pattern (201 bp):
TCTCATCAGGAAGATGACCGCCTCGCTTGTTTTGATTCGCTTCTCTGGATCTCTTCAGGAAGACG
AATCTGGTCCACTTCTCTGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGTCCTGCTTCTC
AGTGTCTCATCAGGAAGCTGGGTTCGAAGATTTGCTCGAGTTTGAGCGTTAAGTTGGTATTCTTC
TCTGTA
Found at i:25759409 original size:59 final size:57
Alignment explanation
Indices: 25759346--25759712 Score: 398
Period size: 59 Copynumber: 6.2 Consensus size: 57
25759336 TTCGAGGGCA
**
25759346 AAAAT-GTAATTTTGCGTGAAATCGGTGTTAAAAATGGAATTTCAGAAAGTTTGGGGGGT
1 AAAATGGTAATTTTG-GTGAAATCGG-GTTAAAAATGGAATTTGGGAAAGTTT-GGGGGT
* * * *
25759405 AAAATGGTAATTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGGAAA-TTCAGGGAGT
1 AAAATGGTAATTTTGGTGAAATC-GGGTTAAAAAT-GGAATTTGGGAAAGTT-TGGGGGT
* * *
25759464 AAAATGGTAATTTTGGTGAAATTCGGGTTAAAAATGGGATTTTGGGAAAATTTAGGGGT
1 AAAATGGTAATTTTGGTGAAA-TCGGGTTAAAAAT-GGAATTTGGGAAAGTTTGGGGGT
* * *
25759523 AAAATGGTAATTTTGGTGAAATTAGGGTT-AAAATGGGATTTTGGAAAGTTTGGGGGT
1 AAAATGGTAATTTTGGTGAAA-TCGGGTTAAAAATGGAATTTGGGAAAGTTTGGGGGT
* * *
25759580 AAAATGGTAAATTTTGGGTGAAATCGAGGTTAAAAATGAGATTTTGGGAAAATTCGGGGGT
1 AAAATGGT-AATTTT-GGTGAAATCG-GGTTAAAAATG-GAATTTGGGAAAGTTTGGGGGT
* * * * * *
25759641 AAAATGGTAATTTTAGTGAAATTGGGGTTGAAAATGGCATTTTGGAAAGTTTGGGGTT
1 AAAATGGTAATTTTGGTGAAA-TCGGGTTAAAAATGGAATTTGGGAAAGTTTGGGGGT
25759699 AAAATGGTAATTTT
1 AAAATGGTAATTTT
25759713 TGGATAGTCC
Statistics
Matches: 265, Mismatches: 31, Indels: 25
0.83 0.10 0.08
Matches are distributed among these distances:
57 26 0.10
58 43 0.16
59 132 0.50
60 39 0.15
61 25 0.09
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.33
Consensus pattern (57 bp):
AAAATGGTAATTTTGGTGAAATCGGGTTAAAAATGGAATTTGGGAAAGTTTGGGGGT
Found at i:25759483 original size:118 final size:112
Alignment explanation
Indices: 25759346--25759712 Score: 450
Period size: 118 Copynumber: 3.1 Consensus size: 112
25759336 TTCGAGGGCA
* **
25759346 AAAAT-GTAATTTTGCGTGAAATCGGTGTTAAAAATGGAATTTCAGAAAGTTTGGGGGGTAAAAT
1 AAAATGGTAATTTTG-GTGAAATCGG-GTTAAAAATGGATTTTGGGAAA-TTT-GGGGGTAAAAT
* * *
25759410 GGTAATTTTGGTAAAATCGGGGTTAAAAATGGGATTTTGGGAAA-TTCAGGGAGT
62 GGTAATTTTGGTGAAATTGGGGTT-AAAATGGGATTTT-GGAAAGTT-TGGG-GT
*
25759464 AAAATGGTAATTTTGGTGAAATTCGGGTTAAAAATGGGATTTTGGGAAAATTTAGGGGTAAAATG
1 AAAATGGTAATTTTGGTGAAA-TCGGGTTAAAAAT-GGATTTTGGG-AAATTTGGGGGTAAAATG
*
25759529 GTAATTTTGGTGAAATTAGGGTTAAAATGGGATTTTGGAAAGTTTGGGGGT
63 GTAATTTTGGTGAAATTGGGGTTAAAATGGGATTTTGGAAAGTTT-GGGGT
*
25759580 AAAATGGTAAATTTTGGGTGAAATCGAGGTTAAAAATGAGATTTTGGGAAAATTCGGGGGTAAAA
1 AAAATGGT-AATTTT-GGTGAAATCG-GGTTAAAAATG-GATTTTGGG-AAATTTGGGGGTAAAA
* *
25759645 TGGTAATTTTAGTGAAATTGGGGTTGAAAATGGCATTTTGGAAAGTTTGGGGTT
61 TGGTAATTTTGGTGAAATTGGGGTT-AAAATGGGATTTTGGAAAGTTTGGGG-T
25759699 AAAATGGTAATTTT
1 AAAATGGTAATTTT
25759713 TGGATAGTCC
Statistics
Matches: 224, Mismatches: 13, Indels: 24
0.86 0.05 0.09
Matches are distributed among these distances:
116 15 0.07
117 28 0.12
118 125 0.56
119 53 0.24
120 3 0.01
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.33
Consensus pattern (112 bp):
AAAATGGTAATTTTGGTGAAATCGGGTTAAAAATGGATTTTGGGAAATTTGGGGGTAAAATGGTA
ATTTTGGTGAAATTGGGGTTAAAATGGGATTTTGGAAAGTTTGGGGT
Found at i:25759716 original size:30 final size:29
Alignment explanation
Indices: 25759390--25759712 Score: 215
Period size: 29 Copynumber: 10.9 Consensus size: 29
25759380 TGGAATTTCA
*
25759390 GAAAGTTTGGGGGGTAAAATGGTAATTTTGG
1 GAAA-TTT-GGGGTTAAAATGGTAATTTTGG
* * * *
25759421 TAAAATCGGGGTTAAAAATGG-GATTTTGG
1 GAAATTTGGGGTT-AAAATGGTAATTTTGG
*
25759450 GAAATTCAGGGAG-TAAAATGGTAATTTTGG
1 GAAATT-TGGG-GTTAAAATGGTAATTTTGG
* *
25759480 TGAAA-TTCGGGTTAAAAATGG-GATTTTGG
1 -GAAATTTGGGGTT-AAAATGGTAATTTTGG
25759509 GAAAATTTAGGGG-TAAAATGGTAATTTTGG
1 G-AAATTT-GGGGTTAAAATGGTAATTTTGG
* *
25759539 TGAAA-TTAGGGTTAAAATGG-GATTTT-G
1 -GAAATTTGGGGTTAAAATGGTAATTTTGG
*
25759566 GAAAGTTTGGGGGTAAAATGGTAAATTTTGGG
1 GAAA-TTTGGGGTTAAAATGGT-AATTTT-GG
* *
25759598 TGAAA-TCGAGGTTAAAAAT-G-AGATTTTGG
1 -GAAATTTGGGGTT-AAAATGGTA-ATTTTGG
* * *
25759627 GAAAATTCGGGGGTAAAATGGTAATTTTAGT
1 G-AAATTTGGGGTTAAAATGGTAATTTT-GG
*
25759658 GAAA-TTGGGGTTGAAAATGG-CATTTT-G
1 GAAATTTGGGGTT-AAAATGGTAATTTTGG
25759685 GAAAGTTTGGGGTTAAAATGGTAATTTT
1 GAAA-TTTGGGGTTAAAATGGTAATTTT
25759713 TGGATAGTCC
Statistics
Matches: 231, Mismatches: 30, Indels: 64
0.71 0.09 0.20
Matches are distributed among these distances:
26 4 0.02
27 5 0.02
28 31 0.13
29 88 0.38
30 72 0.31
31 21 0.09
32 6 0.03
33 4 0.02
ACGTcount: A:0.33, C:0.02, G:0.32, T:0.33
Consensus pattern (29 bp):
GAAATTTGGGGTTAAAATGGTAATTTTGG
Found at i:25760470 original size:18 final size:18
Alignment explanation
Indices: 25760447--25760482 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
25760437 CTCAGCTTTT
25760447 GTTTTTAAACCAGATCTG
1 GTTTTTAAACCAGATCTG
*
25760465 GTTTTTGAACCAGATCTG
1 GTTTTTAAACCAGATCTG
25760483 TGCTTTTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (18 bp):
GTTTTTAAACCAGATCTG
Found at i:25760489 original size:19 final size:18
Alignment explanation
Indices: 25760449--25760489 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
25760439 CAGCTTTTGT
*
25760449 TTTTAAACCAGATCTGGT
1 TTTTAAACCAGATCTGGC
*
25760467 TTTTGAACCAGATCTGTGC
1 TTTTAAACCAGATCTG-GC
25760486 TTTT
1 TTTT
25760490 CCCTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (18 bp):
TTTTAAACCAGATCTGGC
Found at i:25763352 original size:21 final size:23
Alignment explanation
Indices: 25763328--25763374 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
25763318 TCTACTTTAA
25763328 AAAAAAT-A-GAATAAAT-AAAAT
1 AAAAAATCACGAA-AAATAAAAAT
25763349 -AAAAATCACGAAAAATAAAAAT
1 AAAAAATCACGAAAAATAAAAAT
25763371 AAAA
1 AAAA
25763375 TAAAACCATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.27
21 5 0.23
22 8 0.36
23 3 0.14
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (23 bp):
AAAAAATCACGAAAAATAAAAAT
Found at i:25768214 original size:2 final size:2
Alignment explanation
Indices: 25768207--25768239 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25768197 TTAAAAATTA
25768207 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25768240 AAGTACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25768548 original size:12 final size:13
Alignment explanation
Indices: 25768526--25768554 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
25768516 ATAGGAAAAA
25768526 AATTGATAATTAT
1 AATTGATAATTAT
25768539 AATT-ATAATTAT
1 AATTGATAATTAT
25768551 AATT
1 AATT
25768555 TACAACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (13 bp):
AATTGATAATTAT
Found at i:25771937 original size:39 final size:39
Alignment explanation
Indices: 25771841--25771952 Score: 154
Period size: 39 Copynumber: 2.9 Consensus size: 39
25771831 CGCAATACAG
* * * *
25771841 TATTTTCAGTGTTACCGTCAGTTCAGTATTACGTTACGA
1 TATTTACAGTGTTACCGTTAGTTCAGTATTGCATTACGA
*
25771880 TATTTACAATGTTACCGTTAGTTCAGTATTGCATTACGA
1 TATTTACAGTGTTACCGTTAGTTCAGTATTGCATTACGA
*
25771919 TATTTACAGTGTTACCGTTAGCTC-GATATTGCAT
1 TATTTACAGTGTTACCGTTAGTTCAG-TATTGCAT
25771953 CGCAGTGTTT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
38 1 0.02
39 64 0.98
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.41
Consensus pattern (39 bp):
TATTTACAGTGTTACCGTTAGTTCAGTATTGCATTACGA
Found at i:25772760 original size:14 final size:14
Alignment explanation
Indices: 25772741--25772767 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
25772731 TTAAAATGCC
25772741 AAAAAAAGAAGAAG
1 AAAAAAAGAAGAAG
25772755 AAAAAAAGAAGAA
1 AAAAAAAGAAGAA
25772768 ATGTAAAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAAGAAGAAG
Found at i:25777605 original size:24 final size:23
Alignment explanation
Indices: 25777577--25777634 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
25777567 TCCAAACAAC
*
25777577 AAAAATAACAATCAAAACAGCAGT
1 AAAAATAACAAT-AAAACAACAGT
* *
25777601 AAAAATAAAAATAAAACAACATT
1 AAAAATAACAATAAAACAACAGT
*
25777624 AAAAACAACAA
1 AAAAATAACAA
25777635 AAATAGCAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 18 0.62
24 11 0.38
ACGTcount: A:0.71, C:0.14, G:0.03, T:0.12
Consensus pattern (23 bp):
AAAAATAACAATAAAACAACAGT
Found at i:25777673 original size:24 final size:24
Alignment explanation
Indices: 25777627--25777707 Score: 76
Period size: 24 Copynumber: 3.5 Consensus size: 24
25777617 CAACATTAAA
* *
25777627 AACAACAAAAATAGCAACGAAAAC
1 AACAACAAAAATAACAACAAAAAC
*
25777651 AACAACAAAAATAACAGCAAAAAC
1 AACAACAAAAATAACAACAAAAAC
* * * *
25777675 AA-TACGAAAACAACAACCAAAAC
1 AACAACAAAAATAACAACAAAAAC
*
25777698 AATAA-AAAAA
1 AACAACAAAAA
25777708 GTACCAAAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
23 22 0.48
24 24 0.52
ACGTcount: A:0.70, C:0.20, G:0.05, T:0.05
Consensus pattern (24 bp):
AACAACAAAAATAACAACAAAAAC
Found at i:25777684 original size:23 final size:23
Alignment explanation
Indices: 25777658--25777701 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
25777648 AACAACAACA
* *
25777658 AAAATAACAGCAAAAACAATACG
1 AAAACAACAACAAAAACAATACG
*
25777681 AAAACAACAACCAAAACAATA
1 AAAACAACAACAAAAACAATA
25777702 AAAAAAGTAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.68, C:0.20, G:0.05, T:0.07
Consensus pattern (23 bp):
AAAACAACAACAAAAACAATACG
Done.