Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007995.1 Hibiscus syriacus cultivar Beakdansim tig00110445_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 866869
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:2621 original size:17 final size:17
Alignment explanation
Indices: 2592--2633 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
2582 TGTAAACCCT
2592 GTTGACTCGTTGACCAGC-
1 GTTGAC-CGTTGACCA-CA
2610 GTTGACCGTTGACCACA
1 GTTGACCGTTGACCACA
2627 GTTGACC
1 GTTGACC
2634 AACTTGATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 16 0.70
18 6 0.26
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (17 bp):
GTTGACCGTTGACCACA
Found at i:5610 original size:80 final size:81
Alignment explanation
Indices: 5472--5724 Score: 328
Period size: 80 Copynumber: 3.0 Consensus size: 81
5462 GGTAGGCCCA
* * *
5472 TAGGCCCCAAGGCATATCCTTAGGTTGATTACCTTTGCTGTGTGCTTAAGGTAACCCTACGGATC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGATGTGTGCTTAAGGTAACCCTACGGATC
*
5537 TAAGAATATCCTTGGG
66 TAAGGATATCCTTGGG
* *
5553 TAGG-CCCAAGGTATTTCCTTAGGTTGGTTTCCTTTGATGTGTGCTTAAGGTAACCCTACGGATC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGATGTGTGCTTAAGGTAACCCTACGGATC
5617 TAAGGATATCCTTGGGTAGG
66 TAAGGATATCCTT--G--GG
* * * * *
5637 CCCATAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTATGTGCTTAGGGTAACCCTACA
1 ----TAGGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGATGTGTGCTTAAGGTAACCCTACG
5702 GATCTAAGGATATCCTTGGG
62 GATCTAAGGATATCCTTGGG
5722 TAG
1 TAG
5725 TCTCATAGGC
Statistics
Matches: 151, Mismatches: 12, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
80 67 0.44
81 7 0.05
82 1 0.01
84 2 0.01
85 2 0.01
87 1 0.01
88 4 0.03
89 67 0.44
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (81 bp):
TAGGCCCCAAGGTATATCCTTAGGTTGGTTACCTTTGATGTGTGCTTAAGGTAACCCTACGGATC
TAAGGATATCCTTGGG
Found at i:5662 original size:89 final size:89
Alignment explanation
Indices: 5553--5762 Score: 332
Period size: 89 Copynumber: 2.4 Consensus size: 89
5543 TATCCTTGGG
* * * *
5553 TAGG-CCCAAGGTATTTCCTTAGGTTGGTTTCCTTTGATGTGTGCTTAAGGTAACCCTACGGATC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGATATGTGCTTAAGGTAACCCTACAGATC
5617 TAAGGATATCCTTGGGTAGGCCCA
66 TAAGGATATCCTTGGGTAGGCCCA
* *
5641 TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGTTATGTGCTTAGGGTAACCCTACAGATC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGATATGTGCTTAAGGTAACCCTACAGATC
* *
5706 TAAGGATATCCTTGGGTAGTCTCA
66 TAAGGATATCCTTGGGTAGGCCCA
*
5730 TAGGCCCCAAGGTATATCCTTAGGTTGGCTCCC
1 TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCC
5763 CTTTTGGTGT
Statistics
Matches: 112, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
88 4 0.04
89 108 0.96
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.32
Consensus pattern (89 bp):
TAGGCCCCAAGGTATATCCTTAGGTTGGTTCCCTTTGATATGTGCTTAAGGTAACCCTACAGATC
TAAGGATATCCTTGGGTAGGCCCA
Found at i:14184 original size:8 final size:8
Alignment explanation
Indices: 14173--14209 Score: 74
Period size: 8 Copynumber: 4.6 Consensus size: 8
14163 TTTTACATTC
14173 ATATTTTA
1 ATATTTTA
14181 ATATTTTA
1 ATATTTTA
14189 ATATTTTA
1 ATATTTTA
14197 ATATTTTA
1 ATATTTTA
14205 ATATT
1 ATATT
14210 AACTATTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
ATATTTTA
Found at i:14224 original size:11 final size:11
Alignment explanation
Indices: 14208--14233 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
14198 TATTTTAATA
14208 TTAACTATTGT
1 TTAACTATTGT
14219 TTAACTATTGT
1 TTAACTATTGT
14230 TTAA
1 TTAA
14234 TGGCATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (11 bp):
TTAACTATTGT
Found at i:22237 original size:14 final size:16
Alignment explanation
Indices: 22220--22251 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
22210 AGAAAAAAAG
22220 TATAT-TAAAAA-TGT
1 TATATATAAAAATTGT
22234 TATATATAAAAATTGT
1 TATATATAAAAATTGT
22250 TA
1 TA
22252 AAAGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 6 0.38
16 5 0.31
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (16 bp):
TATATATAAAAATTGT
Found at i:22348 original size:25 final size:24
Alignment explanation
Indices: 22297--22375 Score: 65
Period size: 23 Copynumber: 3.2 Consensus size: 24
22287 AGTTTCAAGA
* *
22297 AAAAAATAAAATA-AAAAAACACA-
1 AAAAAATAAAAGAGAAAAAATA-AT
22320 AAAAAATAAAA-AGAAAAGATATAAT
1 AAAAAATAAAAGAGAAAA-A-ATAAT
**
22345 AAAATGTTAAAAGAGAAAAAATAAT
1 AAAA-AATAAAAGAGAAAAAATAAT
22370 AAAAAA
1 AAAAAA
22376 ACAAAACAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
22 1 0.02
23 15 0.33
24 2 0.04
25 15 0.33
26 6 0.13
27 6 0.13
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (24 bp):
AAAAAATAAAAGAGAAAAAATAAT
Found at i:22483 original size:29 final size:30
Alignment explanation
Indices: 22442--22498 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
22432 GGTTGGGGAC
22442 TTAAAAAAGCAAAAACAGACATTTAAAGGA
1 TTAAAAAAGCAAAAACAGACATTTAAAGGA
* *
22472 TTAAACAA-CAAAACCAGACATTTAAAG
1 TTAAAAAAGCAAAAACAGACATTTAAAG
22499 AGCTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.58, C:0.14, G:0.11, T:0.18
Consensus pattern (30 bp):
TTAAAAAAGCAAAAACAGACATTTAAAGGA
Found at i:31185 original size:64 final size:66
Alignment explanation
Indices: 31071--31237 Score: 191
Period size: 65 Copynumber: 2.6 Consensus size: 66
31061 TTTTTCAAAG
*** * * **
31071 TAGTGTACCGATGCACCATTTAATGCATCGATGCAC-CCTTTAATTAATTG-AACTTCGAATGGC
1 TAGTGTACCGATGCA-CATACCATGCATCGATGCACTCCTGTAATTAATTGAAACATCGAAT-AA
31134 TTT
64 TTT
*
31137 T-GTGTACCGATGCACATACCATGCATCGATGCACTCCATGT-GTT-ATTGAAACATCGAATAAT
1 TAGTGTACCGATGCACATACCATGCATCGATGCACTCC-TGTAATTAATTGAAACATCGAATAAT
31199 TT
65 TT
*
31201 TAGTGTACCGATGCACAGACCATGCATCGATGCACTC
1 TAGTGTACCGATGCACATACCATGCATCGATGCACTC
31238 TTGGCTCTTT
Statistics
Matches: 88, Mismatches: 9, Indels: 9
0.83 0.08 0.08
Matches are distributed among these distances:
64 25 0.28
65 60 0.68
66 3 0.03
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.31
Consensus pattern (66 bp):
TAGTGTACCGATGCACATACCATGCATCGATGCACTCCTGTAATTAATTGAAACATCGAATAATT
T
Found at i:31251 original size:65 final size:66
Alignment explanation
Indices: 31117--31281 Score: 198
Period size: 65 Copynumber: 2.6 Consensus size: 66
31107 CCTTTAATTA
* ** *
31117 ATTG-AACTTCGAATGGCTTTT-GTGTACCGATGCACATACCATGCATCGATGCACTCCATGTGT
1 ATTGAAACATCGAATGAATTTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCCATGTGT
31180 T
66 T
*
31181 ATTGAAACATCGAAT-AATTTTAGTGTACCGATGCACAGACCATGCATCGATGCACT-CTTG-GC
1 ATTGAAACATCGAATGAATTTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCCATGTG-
31243 TCT
65 T-T
* * *
31246 TTTGAAACATCGAATGAA-ATTAATGTACCGATGCAC
1 ATTGAAACATCGAATGAATTTTAGTGTACCGATGCAC
31282 TAAGTCTTAT
Statistics
Matches: 88, Mismatches: 8, Indels: 9
0.84 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 12 0.14
65 73 0.83
66 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (66 bp):
ATTGAAACATCGAATGAATTTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCCATGTGT
T
Found at i:31580 original size:28 final size:28
Alignment explanation
Indices: 31540--31630 Score: 173
Period size: 28 Copynumber: 3.2 Consensus size: 28
31530 CAAGTTTGAG
*
31540 CATTTTCAAGCCTATTTCATTCAATATT
1 CATTTTTAAGCCTATTTCATTCAATATT
31568 CATTTTTAAGCCTATTTCATTCAATATT
1 CATTTTTAAGCCTATTTCATTCAATATT
31596 CATTTTTAAGCCTATTTCATTCAATATT
1 CATTTTTAAGCCTATTTCATTCAATATT
31624 CATTTTT
1 CATTTTT
31631 GCTTTCAAGA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 62 1.00
ACGTcount: A:0.27, C:0.19, G:0.03, T:0.51
Consensus pattern (28 bp):
CATTTTTAAGCCTATTTCATTCAATATT
Found at i:31588 original size:17 final size:17
Alignment explanation
Indices: 31566--31616 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
31556 TCATTCAATA
31566 TTCATTTTTAAGCCTAT
1 TTCATTTTTAAGCCTAT
*
31583 TTCA--TTCAA---TA-
1 TTCATTTTTAAGCCTAT
31594 TTCATTTTTAAGCCTAT
1 TTCATTTTTAAGCCTAT
31611 TTCATT
1 TTCATT
31617 CAATATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 12
0.65 0.05 0.30
Matches are distributed among these distances:
11 4 0.15
12 2 0.08
13 4 0.15
15 4 0.15
16 2 0.08
17 10 0.38
ACGTcount: A:0.25, C:0.18, G:0.04, T:0.53
Consensus pattern (17 bp):
TTCATTTTTAAGCCTAT
Found at i:39407 original size:65 final size:65
Alignment explanation
Indices: 39316--39479 Score: 219
Period size: 65 Copynumber: 2.5 Consensus size: 65
39306 CCTTTAATTA
* * *
39316 ATTG-AACTTCGAATGGCTTTT-GTGTACCGATGCACATACCATGCATCGATGCACTCCATGTG-
1 ATTGAAACATCGAAT-GATTTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCC-TG-GC
39378 T-T
63 TCT
39380 ATTGAAACATCGAATGATTTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCT
1 ATTGAAACATCGAATGATTTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCT
* **
39445 TTTGAAACATCGAATGAAATTAGTGTACCGATGCA
1 ATTGAAACATCGAATGATTTTAGTGTACCGATGCA
39480 ACACTAGTGT
Statistics
Matches: 90, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
63 1 0.01
64 12 0.13
65 77 0.86
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (65 bp):
ATTGAAACATCGAATGATTTTAGTGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCT
Found at i:39800 original size:28 final size:28
Alignment explanation
Indices: 39760--39822 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
39750 CAAGTTTGAG
*
39760 CATTTTCAAGCCTATTTCATTCAATATT
1 CATTTTTAAGCCTATTTCATTCAATATT
39788 CATTTTTAAGCCTATTTCATTCAATATT
1 CATTTTTAAGCCTATTTCATTCAATATT
39816 CATTTTT
1 CATTTTT
39823 GCTTTCAAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.27, C:0.19, G:0.03, T:0.51
Consensus pattern (28 bp):
CATTTTTAAGCCTATTTCATTCAATATT
Found at i:41356 original size:14 final size:13
Alignment explanation
Indices: 41323--41369 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
41313 AGTAAGAGAA
41323 TATAATTATATTT
1 TATAATTATATTT
41336 TATTAATTATAATTT
1 TA-TAATTAT-ATTT
*
41351 TATAATAAT-TATT
1 TATAATTATAT-TT
41364 TATAAT
1 TATAAT
41370 CTAACTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.03
13 10 0.33
14 13 0.43
15 6 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATAATTATATTT
Found at i:41361 original size:17 final size:15
Alignment explanation
Indices: 41322--41362 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
41312 TAGTAAGAGA
41322 ATATAATTATATTTT
1 ATATAATTATATTTT
41337 AT-TAATTATAATTTT
1 ATATAATTAT-ATTTT
41352 ATAATAATTAT
1 AT-ATAATTAT
41363 TTATAATCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.30
15 9 0.39
17 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATAATTATATTTT
Found at i:42703 original size:7 final size:7
Alignment explanation
Indices: 42686--42761 Score: 72
Period size: 7 Copynumber: 10.9 Consensus size: 7
42676 CTTAAAACCT
42686 AGAAG-A
1 AGAAGAA
42692 AGAAGAA
1 AGAAGAA
42699 AGAAGACGAA
1 AG-A-A-GAA
42709 AGAAGAA
1 AGAAGAA
42716 AGAAG-A
1 AGAAGAA
42722 AGAA-AGA
1 AGAAGA-A
42729 AGAA-AGA
1 AGAAGA-A
42736 AGAAGAA
1 AGAAGAA
42743 AGAAGAA
1 AGAAGAA
42750 AGAAGAA
1 AGAAGAA
42757 A-AAGA
1 AGAAGA
42762 CCGGGGTGGT
Statistics
Matches: 63, Mismatches: 0, Indels: 14
0.82 0.00 0.18
Matches are distributed among these distances:
6 14 0.22
7 39 0.62
8 3 0.05
9 2 0.03
10 5 0.08
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (7 bp):
AGAAGAA
Found at i:42713 original size:17 final size:17
Alignment explanation
Indices: 42686--42761 Score: 129
Period size: 17 Copynumber: 4.6 Consensus size: 17
42676 CTTAAAACCT
42686 AGAAG-AAGAAGAAAGA
1 AGAAGAAAGAAGAAAGA
*
42702 AGACGAAAGAAGAAAGA
1 AGAAGAAAGAAGAAAGA
42719 AGAAGAAAGAAGAAAGA
1 AGAAGAAAGAAGAAAGA
42736 AGAAGAAAGAAGAAAGA
1 AGAAGAAAGAAGAAAGA
42753 AGAA-AAAGA
1 AGAAGAAAGA
42762 CCGGGGTGGT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
16 9 0.16
17 48 0.84
ACGTcount: A:0.70, C:0.01, G:0.29, T:0.00
Consensus pattern (17 bp):
AGAAGAAAGAAGAAAGA
Found at i:42756 original size:10 final size:10
Alignment explanation
Indices: 42688--42749 Score: 79
Period size: 10 Copynumber: 5.8 Consensus size: 10
42678 TAAAACCTAG
42688 AAGAAGAAGA
1 AAGAAGAAGA
*
42698 AAGAAGACGA
1 AAGAAGAAGA
42708 AAGAAGAAAGAA
1 AAGAAG-AAG-A
42720 GAAGAAAGAAGA
1 -AAG-AAGAAGA
42732 AAGAAGAAGA
1 AAGAAGAAGA
42742 AAGAAGAA
1 AAGAAGAA
42750 AGAAGAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
10 30 0.65
11 5 0.11
12 2 0.04
13 6 0.13
14 3 0.07
ACGTcount: A:0.69, C:0.02, G:0.29, T:0.00
Consensus pattern (10 bp):
AAGAAGAAGA
Found at i:47447 original size:10 final size:11
Alignment explanation
Indices: 47429--47476 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
47419 TATAATAAAT
47429 ATAAAATTTTA
1 ATAAAATTTTA
47440 AT-AAA-TTTA
1 ATAAAATTTTA
47449 ATAAACATTTT-
1 ATAAA-ATTTTA
*
47460 ATAAAATTTCA
1 ATAAAATTTTA
47471 ATAAAA
1 ATAAAA
47477 ATTTGATGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
9 6 0.19
10 9 0.28
11 14 0.44
12 3 0.09
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAAAATTTTA
Found at i:47460 original size:21 final size:21
Alignment explanation
Indices: 47429--47476 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
47419 TATAATAAAT
47429 ATAAAATTTTA-ATAAATTT-A
1 ATAAAATTTTATA-AAATTTCA
47449 ATAAACATTTTATAAAATTTCA
1 ATAAA-ATTTTATAAAATTTCA
47471 ATAAAA
1 ATAAAA
47477 ATTTGATGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
20 5 0.20
21 13 0.52
22 7 0.28
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAAAATTTTATAAAATTTCA
Found at i:47480 original size:22 final size:21
Alignment explanation
Indices: 47426--47480 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
47416 CATTATAATA
47426 AATATAAAATTTTAATAAATTT
1 AATA-AAAATTTTAATAAATTT
*
47448 AATAAACATTTT-ATAAAATTT
1 AATAAAAATTTTAAT-AAATTT
47469 CAATAAAAATTT
1 -AATAAAAATTT
47481 GATGATCACT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 13 0.45
22 14 0.48
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AATAAAAATTTTAATAAATTT
Found at i:59192 original size:17 final size:16
Alignment explanation
Indices: 59167--59209 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
59157 CTTTTCAAAC
*
59167 TCTAATTATTATTTTAT
1 TCTATTTATTATTTT-T
59184 TCTATTTATTATTTTT
1 TCTATTTATTATTTTT
59200 TCTACTTTAT
1 TCTA-TTTAT
59210 CTTTATCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (16 bp):
TCTATTTATTATTTTT
Found at i:63030 original size:17 final size:16
Alignment explanation
Indices: 63005--63047 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
62995 CTTTTCAAAC
*
63005 TCTAATTATTATTTTAT
1 TCTATTTATTATTTT-T
63022 TCTATTTATTATTTTT
1 TCTATTTATTATTTTT
63038 TCTACTTTAT
1 TCTA-TTTAT
63048 CTTTATCTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.23, C:0.09, G:0.00, T:0.67
Consensus pattern (16 bp):
TCTATTTATTATTTTT
Found at i:66718 original size:186 final size:185
Alignment explanation
Indices: 66405--66757 Score: 591
Period size: 186 Copynumber: 1.9 Consensus size: 185
66395 ATTAAAAAGT
* *
66405 TTATTTTATAACTGACGTTGTCATTGAAAGCCATCTACTCTCACTTGAACAATTTCAATTTTTTC
1 TTATTTTATAACTAACGTTGTCATTGAAAGCCATCTACTCTCACTTGAACAATTCCAATTTTTTC
* * * *
66470 TTCATTTTTTGTTATCTAATTTTTATATACAATTGAATCATCAACCAATTATTTACTATCAAATT
66 TTCATTTTTTGATACCTAATTTTTATATACAATTGAACCATCAACCAATTATTTAATATCAAATT
* *
66535 ATGG-CATATTAAATGAATAAGTTATAACCTACATATTCCAATTATTTAATACCAA
131 A-GGTCAGACTAAATGAATAAGTTATAACCTACATATTCCAATTATTTAATACCAA
* *
66590 TTATTTTATAACTAACGTTGTCATTGCAGGCCATCTACTCTCACTTGAACAATTCCAATTTTTTT
1 TTATTTTATAACTAACGTTGTCATTGAAAGCCATCTACTCTCACTTGAACAATTCCAA-TTTTTT
66655 CTTCATTTTTTGATACCTAATTTTTATATACAATTGAACCATCAACCAATTATTTAATATCAAAT
65 CTTCATTTTTTGATACCTAATTTTTATATACAATTGAACCATCAACCAATTATTTAATATCAAAT
66720 TAGGTCAGACTAAATGAATAAGTTATAACCTACATATT
130 TAGGTCAGACTAAATGAATAAGTTATAACCTACATATT
66758 GAAATAAGTT
Statistics
Matches: 156, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
185 56 0.36
186 100 0.64
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (185 bp):
TTATTTTATAACTAACGTTGTCATTGAAAGCCATCTACTCTCACTTGAACAATTCCAATTTTTTC
TTCATTTTTTGATACCTAATTTTTATATACAATTGAACCATCAACCAATTATTTAATATCAAATT
AGGTCAGACTAAATGAATAAGTTATAACCTACATATTCCAATTATTTAATACCAA
Found at i:70023 original size:5 final size:6
Alignment explanation
Indices: 70007--70031 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
69997 AATTTAACAA
70007 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
70032 AAACGGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:84938 original size:4 final size:4
Alignment explanation
Indices: 84921--84952 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
84911 TCTTTTCTTT
*
84921 TCCC TCCC TTCC TCCC TCCC TCCC TCCC TCCC
1 TCCC TCCC TCCC TCCC TCCC TCCC TCCC TCCC
84953 ATTGAACTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.72, G:0.00, T:0.28
Consensus pattern (4 bp):
TCCC
Found at i:89255 original size:2 final size:2
Alignment explanation
Indices: 89248--89302 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
89238 AGGGTGGAAG
89248 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
89290 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
89303 TTCAGGTCGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:89754 original size:15 final size:16
Alignment explanation
Indices: 89721--89755 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
89711 TTATTGAATT
89721 AATTATATTACTATAA
1 AATTATATTACTATAA
*
89737 AATTATATTA-TGTAA
1 AATTATATTACTATAA
89752 AATT
1 AATT
89756 TTAAATGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
AATTATATTACTATAA
Found at i:93461 original size:3 final size:3
Alignment explanation
Indices: 93453--93501 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
93443 TGTAATATAT
* **
93453 TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
93499 TAA
1 TAA
93502 AATGACGATA
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
2 3 0.08
3 35 0.92
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:93910 original size:40 final size:41
Alignment explanation
Indices: 93674--93910 Score: 115
Period size: 40 Copynumber: 5.6 Consensus size: 41
93664 GGCGACACTG
* * *
93674 CTCATACATGATGAAGAGTTCGGGTCGTCTAAGGG-TGACACAA
1 CTCATACGTGATGAAGAGTTC---TGGTCTAAGGGATGACACGA
* * ** * **
93717 TTCCTACGTGATGAAGAAATCTGGTC-GAGGGATGACATTA
1 CTCATACGTGATGAAGAGTTCTGGTCTAAGGGATGACACGA
** * *
93757 CTCATATATGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGG
1 CTCATACGTGATGAAGAGTTC-TGG---TCT-AAGG-GATGACACGA
* * * * *
93804 TTCCTACGTGATGAGGACG-ACTGGTTATCTAAGGG-TGACACGG
1 CTCATACGTGATGAAGA-GTTCTGG---TCTAAGGGATGACACGA
* * **
93847 CTCCTACGTGATGAGGAAATCTGGTC-AAGGGATGACACGA
1 CTCATACGTGATGAAGAGTTCTGGTCTAAGGGATGACACGA
93887 CTCATACGTGATGAAGAGTTCTGG
1 CTCATACGTGATGAAGAGTTCTGG
93911 CCATCTTTAG
Statistics
Matches: 146, Mismatches: 37, Indels: 25
0.70 0.18 0.12
Matches are distributed among these distances:
39 9 0.06
40 54 0.37
41 3 0.02
43 43 0.29
44 3 0.02
45 4 0.03
46 10 0.07
47 19 0.13
48 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (41 bp):
CTCATACGTGATGAAGAGTTCTGGTCTAAGGGATGACACGA
Found at i:94162 original size:40 final size:41
Alignment explanation
Indices: 93964--94163 Score: 149
Period size: 40 Copynumber: 4.8 Consensus size: 41
93954 ACGTCTAGTT
93964 ATCTAGGGG-TGACACGGCTCCTACGTGATGAAGAGATCTGG
1 ATCT-GGGGATGACACGGCTCCTACGTGATGAAGAGATCTGG
* * *
94005 -TC-GGGGAATGACACGGCTCATACGTGATGAAGAGTTATGG
1 ATCTGGGG-ATGACACGGCTCCTACGTGATGAAGAGATCTGG
* * * * * *
94045 CCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACG-GCTGG
1 --ATCT---GGGGATGACACGGCTCCTACGTGATGAAGA-GATCTGG
** *
94091 TTATCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGG
1 --ATCTGGGGATGACACGGCTCCTACGTGATGAAGAGATCTGG
* *
94134 -TCTGGGGATGACACGGTTCCTACATGATGA
1 ATCTGGGGATGACACGGCTCCTACGTGATGA
94164 GGACGGCTGG
Statistics
Matches: 121, Mismatches: 27, Indels: 23
0.71 0.16 0.13
Matches are distributed among these distances:
38 4 0.03
40 56 0.46
42 1 0.01
43 28 0.23
46 28 0.23
47 4 0.03
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (41 bp):
ATCTGGGGATGACACGGCTCCTACGTGATGAAGAGATCTGG
Found at i:94179 original size:129 final size:128
Alignment explanation
Indices: 93701--94163 Score: 604
Period size: 134 Copynumber: 3.5 Consensus size: 128
93691 GTTCGGGTCG
*** ** *
93701 TCTAAGGGTGACACAATTCCTACGTGATGAAGAAATCTGGTCGAGGGATGACATTACTCATATAT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAAGAAATCTGGTCG-GGGATGACACGACTCATACAT
*
93766 GATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTA
65 GATGAAGAGTTC-TGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTA
* * *
93831 TCTAAGGGTGACACGGCTCCTACGTGATGAGGAAATCTGGTCAAGGGATGACACGACTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAAGAAATCTGGTC-GGGGATGACACGACTCATACAT
*
93896 GATGAAGAGTTCTGGCCATCTTTAGGAAGG-GCAATAACATGGTTCCTACGTGATGAGGACGTCT
65 GATGAAGAGTTCTGGCCATC--TA--AAGGTG--ATAACATGGTTCCTACGTGATGAGGACGACT
*
93960 AGTTA
124 GGTTA
* * * *
93965 TCTAGGGGTGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAAGAAATCTGGTCGGGG-ATGACACGACTCATACAT
* *
94030 GATGAAGAGTTATGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGGCTGGTTA
65 GATGAAGAGTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTA
* * * ** *
94094 TCTATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACAT
1 TCTAAGGGTGACACGGCTCCTACGTGATGAAGAAATCTGGTC-GGGGATGACACGACTCATACAT
94159 GATGA
65 GATGA
94164 GGACGGCTGG
Statistics
Matches: 298, Mismatches: 25, Indels: 21
0.87 0.07 0.06
Matches are distributed among these distances:
129 102 0.34
130 75 0.25
131 3 0.01
132 3 0.01
133 7 0.02
134 108 0.36
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (128 bp):
TCTAAGGGTGACACGGCTCCTACGTGATGAAGAAATCTGGTCGGGGATGACACGACTCATACATG
ATGAAGAGTTCTGGCCATCTAAAGGTGATAACATGGTTCCTACGTGATGAGGACGACTGGTTA
Found at i:94232 original size:28 final size:28
Alignment explanation
Indices: 94212--94273 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
94202 AAACCAAATT
94212 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* * *
94240 AAAGATTTGTTTCAAAAAAAATAAACTC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
94268 AAAGAT
1 AAAGAT
94274 GATATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.53, C:0.13, G:0.10, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:95265 original size:30 final size:30
Alignment explanation
Indices: 95229--95292 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 30
95219 GAGACAAAAA
*
95229 TTTTGTTTCCAAAGAAACAGA-CTCAAAGAT
1 TTTTGTTTCAAAAGAAACA-ATCTCAAAGAT
95259 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAATCTCAAAGAT
95289 TTTT
1 TTTT
95293 TCACAAAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 1 0.03
30 31 0.97
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.36
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAATCTCAAAGAT
Found at i:95354 original size:52 final size:51
Alignment explanation
Indices: 95280--95380 Score: 159
Period size: 50 Copynumber: 2.0 Consensus size: 51
95270 AAGAAACAAT
*
95280 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAACACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTC-A-AGAGACAAAACTTTGTTTCAGA
*
95333 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGACAAAACTTTGTTTCA
95381 AAATAAATAG
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
50 19 0.41
51 1 0.02
52 18 0.39
53 8 0.17
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.33
Consensus pattern (51 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGACAAAACTTTGTTTCAGA
Found at i:95407 original size:28 final size:28
Alignment explanation
Indices: 95376--95501 Score: 128
Period size: 28 Copynumber: 4.5 Consensus size: 28
95366 CAAAACTTTG
* *
95376 TTTCAAAATAAATAGACTCAAAGATTTT
1 TTTCAAAAGAAACAGACTCAAAGATTTT
*
95404 TTTCAAAAGAAACA-ACTCAAATATATTT
1 TTTCAAAAGAAACAGACTCAAAGAT-TTT
* * * *
95432 ATTCAAAAGGAACAAACTCCAAGATTTT
1 TTTCAAAAGAAACAGACTCAAAGATTTT
* *
95460 TATTCAAAAGGAACAGACTCAAAGATTTA
1 T-TTCAAAAGAAACAGACTCAAAGATTTT
* *
95489 TCTCAAGAGAAAC
1 TTTCAAAAGAAAC
95502 TGTCTCCAGA
Statistics
Matches: 81, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
27 9 0.11
28 39 0.48
29 33 0.41
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.28
Consensus pattern (28 bp):
TTTCAAAAGAAACAGACTCAAAGATTTT
Found at i:95450 original size:29 final size:28
Alignment explanation
Indices: 95391--95487 Score: 124
Period size: 29 Copynumber: 3.4 Consensus size: 28
95381 AAATAAATAG
* *
95391 ACTCAAAGATTTTTTTCAAAAGAAAC-A
1 ACTCAAAGATTTTATTCAAAAGGAACAA
*
95418 ACTCAAATATATTTATTCAAAAGGAACAA
1 ACTCAAAGAT-TTTATTCAAAAGGAACAA
* *
95447 ACTCCAAGATTTTTATTCAAAAGGAACAG
1 ACTCAAAGA-TTTTATTCAAAAGGAACAA
95476 ACTCAAAGATTT
1 ACTCAAAGATTT
95488 ATCTCAAGAG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.15
28 17 0.28
29 33 0.55
30 1 0.02
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (28 bp):
ACTCAAAGATTTTATTCAAAAGGAACAA
Found at i:95885 original size:36 final size:36
Alignment explanation
Indices: 95801--95904 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
95791 AAAGGAAAAA
* * *
95801 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
95835 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
95871 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
95905 ACAATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:95913 original size:36 final size:36
Alignment explanation
Indices: 95803--95920 Score: 98
Period size: 36 Copynumber: 3.3 Consensus size: 36
95793 AGGAAAAATG
* * * * *
95803 TCTCAAGCGAGACGAAATTTG-CTTTA-AGATATAG
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAACAA
** ***
95837 TCTCAAATGAGACAAAATTTGTTTTTAGAGAAATTG
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAACAA
*
95873 TCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAACAA
1 TCTCAAGCGAGACAAAATTTGTTTTTAGAG-AAACAA
*
95909 TCTCAAGTGAGA
1 TCTCAAGCGAGA
95921 TCAACTTTGT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
34 18 0.26
35 7 0.10
36 43 0.63
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (36 bp):
TCTCAAGCGAGACAAAATTTGTTTTTAGAGAAACAA
Found at i:96051 original size:105 final size:101
Alignment explanation
Indices: 95872--96103 Score: 283
Period size: 105 Copynumber: 2.2 Consensus size: 101
95862 TAGAGAAATT
95872 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
*
95936 GTGAAACAAATTCGAA-ATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTC-AAGATTTGGATCTCAAAGGAAAAAG
* *
95974 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * * *
96038 TAA-GTGAATCAAATTCAAGGTTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAGATTTGGATCTCAAAGGAAAAAG
*
96079 GTCTCAAGCGAGACGAAGTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTT
96104 AAGAGAATTT
Statistics
Matches: 114, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 6 0.05
105 75 0.66
106 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAGATTTGGATCTCAAAGGAAAAAG
Found at i:96236 original size:272 final size:267
Alignment explanation
Indices: 95639--96249 Score: 757
Period size: 272 Copynumber: 2.3 Consensus size: 267
95629 TTTTGAAAAA
* * * * * *
95639 CTCAAGTGATATTAATTTTGTTTCAA-GT-ACAACAAATT-TAAATTTGTATCTCAGAGAAAAAT
1 CTCAAGTGAGATCAACTTTGTTT-AATGTGA-AACAAATTCAAAATTTGTATCTCAAAGAAAAAG
* *
95701 GTCTCAAGTGAAACGAAATTTGTTTCGAAATAAACAACAATATCAAGTGAGATTTTGTTTTAAGT
64 GTCTCAAGCGAAACGAAATTTGTTTCGAAAGAAACAACAATATCAAGTGAGATTTTGTTTTAAGT
95766 GAAACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTTTAAG
129 GAAACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTTTAAG
* * * * *
95831 ATATAGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACAAAGTTTGTT
194 AAATAGTCTCAAATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAA-----TA
95896 TTTGAGAAAACAAT
254 TTTGAGAAAACAAT
* * *
95910 CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAGG
1 CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAA-GAAAAAGG
* * *
95975 TCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTTT
65 TCTCAAGCGAAACGAAATTTGTTTCGAAAGAAACAACAATATCAA-GTGAG----ATTTTGTTTT
* ** * *
96039 AAGTGAATCAAATTCAAGGTTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAGTTTG-TT
125 AAGTGAAACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTT
* * * * *
96103 TAAGAGAATTTGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAA-
190 TAAGA-AA-TAGTCTCAAATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAAT
*
96167 ATTTGAGAAAACGAT
253 ATTTGAGAAAACAAT
* *
96182 CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAATGAAAAATGT
1 CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAAGAAAAAGGT
96247 CTC
66 CTC
96250 CAGTGAGGCG
Statistics
Matches: 295, Mismatches: 34, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
270 2 0.01
271 40 0.14
272 83 0.28
273 48 0.16
276 7 0.02
277 68 0.23
278 47 0.16
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.32
Consensus pattern (267 bp):
CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCAAAATTTGTATCTCAAAGAAAAAGGT
CTCAAGCGAAACGAAATTTGTTTCGAAAGAAACAACAATATCAAGTGAGATTTTGTTTTAAGTGA
AACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTTTAAGAA
ATAGTCTCAAATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAATATTTGAGA
AAACAAT
Found at i:96301 original size:36 final size:35
Alignment explanation
Indices: 96261--96378 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 35
96251 AGTGAGGCGG
96261 AATTTGTTTTTCAAGAAATTGTCTCAAACGAGACAA
1 AATTTGTTTTT-AAGAAATTGTCTCAAACGAGACAA
* *
96297 AATTTGTTTTT-AGAAAGCTGTCTCAATCGAGACAA
1 AATTTGTTTTTAAGAAA-TTGTCTCAAACGAGACAA
** *
96332 AATTTGCTTTGAAAGAAATTGTCTCAAGCGAGACAAA
1 AATTTG-TTTTTAAGAAATTGTCTCAAACGAGAC-AA
96369 AATTTGTTTT
1 AATTTGTTTT
96379 AAAATTCTCA
Statistics
Matches: 71, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
34 5 0.07
35 22 0.31
36 31 0.44
37 13 0.18
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (35 bp):
AATTTGTTTTTAAGAAATTGTCTCAAACGAGACAA
Found at i:96972 original size:4 final size:4
Alignment explanation
Indices: 96923--96960 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
96913 TTTATGTATC
*
96923 ATGT ATGT ATG- -TGT ATGT ATGT ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
96961 GTTGATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:101323 original size:31 final size:32
Alignment explanation
Indices: 101267--101328 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
101257 TGACAAAATG
*
101267 ACACAAACAAAAGAGAGGAAATAAGTTAGTAT
1 ACACAAACAAAAGAGAGAAAATAAGTTAGTAT
101299 ACACAAACAAAAGAGA-AAAATAAGTTAGTA
1 ACACAAACAAAAGAGAGAAAATAAGTTAGTA
101329 CATGTAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.60, C:0.10, G:0.16, T:0.15
Consensus pattern (32 bp):
ACACAAACAAAAGAGAGAAAATAAGTTAGTAT
Found at i:104783 original size:3 final size:3
Alignment explanation
Indices: 104769--104827 Score: 77
Period size: 3 Copynumber: 20.0 Consensus size: 3
104759 CAAAAATTTG
**
104769 TAA TATA TAA TAA TAA -AA TAA TAA CGA TAA TAA TAA TAA TAA TAA
1 TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
104814 TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA
104828 CGATAAAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 4 0.08
3 42 0.86
4 3 0.06
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:104800 original size:9 final size:9
Alignment explanation
Indices: 104777--104833 Score: 55
Period size: 9 Copynumber: 6.6 Consensus size: 9
104767 TGTAATATAT
104777 AATAATAA-
1 AATAATAAC
104785 AATAATAAC
1 AATAATAAC
* *
104794 GATAATAAT
1 AATAATAAC
*
104803 AATAATAAT
1 AATAATAAC
*
104812 AATAATAAT
1 AATAATAAC
104821 AA-AATAAC
1 AATAATAAC
*
104829 GATAA
1 AATAA
104834 AAAAAAACCC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
8 14 0.33
9 28 0.67
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (9 bp):
AATAATAAC
Found at i:106932 original size:147 final size:147
Alignment explanation
Indices: 106665--106958 Score: 588
Period size: 147 Copynumber: 2.0 Consensus size: 147
106655 CATACCCCAA
106665 AATTTTTATCTAAAATTCATTTAATTGTTTTCCAGACTAAAAGGCAAATTTTTAAAGACTCTTGG
1 AATTTTTATCTAAAATTCATTTAATTGTTTTCCAGACTAAAAGGCAAATTTTTAAAGACTCTTGG
106730 CTAAATTCAAAAGTTTGAGAAGTTTAGAGACTTAACCTCGAATTAACCCATTTTTCTAATCAGCT
66 CTAAATTCAAAAGTTTGAGAAGTTTAGAGACTTAACCTCGAATTAACCCATTTTTCTAATCAGCT
106795 TTAAAAAAATGTAAAAT
131 TTAAAAAAATGTAAAAT
106812 AATTTTTATCTAAAATTCATTTAATTGTTTTCCAGACTAAAAGGCAAATTTTTAAAGACTCTTGG
1 AATTTTTATCTAAAATTCATTTAATTGTTTTCCAGACTAAAAGGCAAATTTTTAAAGACTCTTGG
106877 CTAAATTCAAAAGTTTGAGAAGTTTAGAGACTTAACCTCGAATTAACCCATTTTTCTAATCAGCT
66 CTAAATTCAAAAGTTTGAGAAGTTTAGAGACTTAACCTCGAATTAACCCATTTTTCTAATCAGCT
106942 TTAAAAAAATGTAAAAT
131 TTAAAAAAATGTAAAAT
106959 GATTGACTGG
Statistics
Matches: 147, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
147 147 1.00
ACGTcount: A:0.39, C:0.14, G:0.11, T:0.37
Consensus pattern (147 bp):
AATTTTTATCTAAAATTCATTTAATTGTTTTCCAGACTAAAAGGCAAATTTTTAAAGACTCTTGG
CTAAATTCAAAAGTTTGAGAAGTTTAGAGACTTAACCTCGAATTAACCCATTTTTCTAATCAGCT
TTAAAAAAATGTAAAAT
Found at i:117812 original size:45 final size:43
Alignment explanation
Indices: 117752--117885 Score: 141
Period size: 45 Copynumber: 3.0 Consensus size: 43
117742 ATCATTAATC
117752 TTTTCAATCTCATTTTTATATTTATAATTGATGACCCTAATTTTT
1 TTTTCAATCTCATTTTTATATTTATAATTGA-GACCCTAA-TTTT
117797 TTTTCAATCTCATTTTT-TAACTTTATAATTGA-ACTCCTAA-TTT
1 TTTTCAATCTCATTTTTAT-A-TTTATAATTGAGAC-CCTAATTTT
* ** *
117840 TTTT-AATCTTACTTTTTACCTTTATAATTGAGACCCCTAATCTT
1 TTTTCAATCTCA-TTTTTATATTTATAATTGAGA-CCCTAATTTT
117884 TT
1 TT
117886 ACTCACTTTT
Statistics
Matches: 77, Mismatches: 4, Indels: 17
0.79 0.04 0.17
Matches are distributed among these distances:
42 17 0.22
43 18 0.23
44 8 0.10
45 23 0.30
46 11 0.14
ACGTcount: A:0.26, C:0.16, G:0.04, T:0.54
Consensus pattern (43 bp):
TTTTCAATCTCATTTTTATATTTATAATTGAGACCCTAATTTT
Found at i:117886 original size:42 final size:44
Alignment explanation
Indices: 117750--117903 Score: 153
Period size: 42 Copynumber: 3.6 Consensus size: 44
117740 GTATCATTAA
**
117750 TCTTTTCAATCTCA-TTTTTATATTTATAATTGATGA-CCCTAATTT
1 TCTTTTCAATCTCACTTTTTACCTTTATAATTGA-GACCCCTAA--T
* * * *
117795 TTTTTTCAATCTCATTTTTTAACTTTATAATTGA-ACTCCTAAT
1 TCTTTTCAATCTCACTTTTTACCTTTATAATTGAGACCCCTAAT
* *
117838 T-TTTTTAATCTTACTTTTTACCTTTATAATTGAGACCCCTAA-
1 TCTTTTCAATCTCACTTTTTACCTTTATAATTGAGACCCCTAAT
117880 TCTTTT--A-CTCACTTTTTACCTTTA
1 TCTTTTCAATCTCACTTTTTACCTTTA
117904 AAATCGAGGC
Statistics
Matches: 95, Mismatches: 10, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
40 16 0.17
41 1 0.01
42 29 0.31
43 13 0.14
44 1 0.01
45 18 0.19
46 17 0.18
ACGTcount: A:0.25, C:0.18, G:0.03, T:0.53
Consensus pattern (44 bp):
TCTTTTCAATCTCACTTTTTACCTTTATAATTGAGACCCCTAAT
Found at i:118219 original size:43 final size:44
Alignment explanation
Indices: 118172--118495 Score: 229
Period size: 43 Copynumber: 7.4 Consensus size: 44
118162 TTTATTTTTA
* * * *
118172 TTTTTATATTTATAATTGATGTCCCCAATTTTTGT-AATCACAC
1 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCAC
* * *
118215 TTTTTATTTTTATAATTG-GGACCATTAA-TTTTTTCAATCTCAC
1 TTTTTATATTTATAATTGATGACC-CTAATTTTTTTCAATCTCAC
118258 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCAC
1 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCAC
* * *
118302 TTTTTACATTTATAATTGA--ACTTCTAATTTTTTT-AATCTTAC
1 TTTTTATATTTATAATTGATGAC-CCTAATTTTTTTCAATCTCAC
* * * *
118344 TTTTTACATTTATAATTGAGGCCCCTAGGCCCTAGTTTTTTT-AATATCAC
1 TTTTTATATTTATAATTGA------T-GACCCTAATTTTTTTCAATCTCAC
* ** * ** *
118394 TTTTGACCTTTAAAATTGA-GGTCTTAATTTTTTT-AATCTCAC
1 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCAC
** * * * *
118436 TTTTTACCTTTAAAATTGAGGTCCTTAATTTTTTTCAATCAT-AC
1 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATC-TCAC
*
118480 TTTTTA-CTTTATAATT
1 TTTTTATATTTATAATT
118496 TAAACCCCTA
Statistics
Matches: 235, Mismatches: 29, Indels: 34
0.79 0.10 0.11
Matches are distributed among these distances:
42 73 0.31
43 79 0.34
44 49 0.21
45 1 0.00
50 32 0.14
51 1 0.00
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (44 bp):
TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCAC
Found at i:118324 original size:21 final size:21
Alignment explanation
Indices: 118300--118362 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
118290 TTTCAATCTC
118300 ACTTTTTACATTTATAATTGA
1 ACTTTTTACATTTATAATTGA
* * ** * *
118321 ACTTCTAATTTTTTTAATCT-T
1 ACTTTTTACATTTATAAT-TGA
118342 ACTTTTTACATTTATAATTGA
1 ACTTTTTACATTTATAATTGA
118363 GGCCCCTAGG
Statistics
Matches: 28, Mismatches: 12, Indels: 4
0.64 0.27 0.09
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.56
Consensus pattern (21 bp):
ACTTTTTACATTTATAATTGA
Found at i:118370 original size:86 final size:84
Alignment explanation
Indices: 118172--118495 Score: 278
Period size: 86 Copynumber: 3.7 Consensus size: 84
118162 TTTATTTTTA
* * * * *
118172 TTTTTATATTTATAATTGATGTCCCC-AATTTTTGTAATCACACTTTTTATTTTTATAATTGGGA
1 TTTTTACATTTATAATTGA-GGCCCCTAATTTTTTTAATCTCACTTTTTA-CTTTATAATT--GA
* *
118236 CCAT-TAATTTTTTCAATCTCAC
62 ACATCTAATTTTTTTAATCTCAC
* * *
118258 TTTTTATATTTATAATTGATGACCCTAATTTTTTTCAATCTCACTTTTTACATTTATAATTGAAC
1 TTTTTACATTTATAATTGAGGCCCCTAATTTTTTT-AATCTCACTTTTTAC-TTTATAATTGAAC
* *
118323 TTCTAATTTTTTTAATCTTAC
64 ATCTAATTTTTTTAATCTCAC
* * *
118344 TTTTTACATTTATAATTGAGGCCCCTAGGCCCTAGTTTTTTTAATATCACTTTTGACCTTTAAAA
1 TTTTTACATTTATAATTGAGGCCCCTA------A-TTTTTTTAATCTCACTTTTTA-CTTTATAA
**
118409 TTG-AGGTCTTAATTTTTTTAATCTCAC
58 TTGAACATC-TAATTTTTTTAATCTCAC
* * * *
118436 TTTTTACCTTTAAAATTGAGGTCCTTAATTTTTTTCAATCAT-ACTTTTTACTTTATAATT
1 TTTTTACATTTATAATTGAGGCCCCTAATTTTTTT-AATC-TCACTTTTTACTTTATAATT
118496 TAAACCCCTA
Statistics
Matches: 197, Mismatches: 26, Indels: 31
0.78 0.10 0.12
Matches are distributed among these distances:
85 23 0.12
86 78 0.40
87 23 0.12
91 3 0.02
92 62 0.31
93 8 0.04
ACGTcount: A:0.27, C:0.15, G:0.07, T:0.52
Consensus pattern (84 bp):
TTTTTACATTTATAATTGAGGCCCCTAATTTTTTTAATCTCACTTTTTACTTTATAATTGAACAT
CTAATTTTTTTAATCTCAC
Found at i:118422 original size:92 final size:93
Alignment explanation
Indices: 118280--118456 Score: 241
Period size: 92 Copynumber: 1.9 Consensus size: 93
118270 TAATTGATGA
* * * *
118280 CCCTAATTTTTTTCAATCTCACTTTTTACATTTATAATTGAACTTCTAATTTTTTTAATCTTACT
1 CCCTAATTTTTTTCAATATCACTTTTGACATTTAAAATTGAACTTCTAATTTTTTTAATCTCACT
*
118345 TTTTACATTTATAATTGAGGCCCCTAGG
66 TTTTACATTTAAAATTGAGGCCCCTAGG
* * **
118373 CCCTAGTTTTTTT-AATATCACTTTTGACCTTTAAAATTG-AGGTCTTAATTTTTTTAATCTCAC
1 CCCTAATTTTTTTCAATATCACTTTTGACATTTAAAATTGAACTTC-TAATTTTTTTAATCTCAC
*
118436 TTTTTACCTTTAAAATTGAGG
65 TTTTTACATTTAAAATTGAGG
118457 TCCTTAATTT
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
91 3 0.04
92 58 0.79
93 12 0.16
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.49
Consensus pattern (93 bp):
CCCTAATTTTTTTCAATATCACTTTTGACATTTAAAATTGAACTTCTAATTTTTTTAATCTCACT
TTTTACATTTAAAATTGAGGCCCCTAGG
Found at i:118508 original size:43 final size:43
Alignment explanation
Indices: 118373--118509 Score: 118
Period size: 42 Copynumber: 3.2 Consensus size: 43
118363 GGCCCCTAGG
* * * **
118373 CCCTAGTTTTTTTAATATCACTTTTGACCTTTAAAATTG-AGG
1 CCCTAATTTTTTTAATCTCACTTTTTACCTTTAAAATTGAAAC
* * ***
118415 TCTTAATTTTTTTAATCTCACTTTTTACCTTTAAAATTGAGGT
1 CCCTAATTTTTTTAATCTCACTTTTTACCTTTAAAATTGAAAC
* * *
118458 CCTTAATTTTTTTCAATCAT-ACTTTTTA-CTTTATAATTTAAAC
1 CCCTAATTTTTTT-AATC-TCACTTTTTACCTTTAAAATTGAAAC
118501 CCCTAATTT
1 CCCTAATTT
118510 AATCATTTTC
Statistics
Matches: 78, Mismatches: 14, Indels: 5
0.80 0.14 0.05
Matches are distributed among these distances:
42 34 0.44
43 31 0.40
44 12 0.15
45 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (43 bp):
CCCTAATTTTTTTAATCTCACTTTTTACCTTTAAAATTGAAAC
Found at i:118636 original size:21 final size:21
Alignment explanation
Indices: 118612--118654 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
118602 TCAAGACCCA
*
118612 GAAAATATCTGAGACGACTCT
1 GAAAATATCTCAGACGACTCT
* *
118633 GAAAATGTCTCAGACGGCTCT
1 GAAAATATCTCAGACGACTCT
118654 G
1 G
118655 GGTGTAACAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (21 bp):
GAAAATATCTCAGACGACTCT
Found at i:123809 original size:29 final size:29
Alignment explanation
Indices: 123766--123848 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
123756 CTCACCTAAC
123766 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
123796 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
123825 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
123849 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:127170 original size:186 final size:185
Alignment explanation
Indices: 126857--127209 Score: 591
Period size: 186 Copynumber: 1.9 Consensus size: 185
126847 ATTAAAAAGT
* *
126857 TTATTTTATAACTGACGTTGTCATTGAAAGCCATCTACTCTCACTTGAACAATTTCAATTTTTTC
1 TTATTTTATAACTAACGTTGTCATTGAAAGCCATCTACTCTCACTTGAACAATTCCAATTTTTTC
* * * *
126922 TTCATTTTTTGTTATCTAATTTTTATATACAATTGAATCATCAACCAATTATTTACTATCAAATT
66 TTCATTTTTTGATACCTAATTTTTATATACAATTGAACCATCAACCAATTATTTAATATCAAATT
* *
126987 ATGG-CATATTAAATGAATAAGTTATAACCTACATATTCCAATTATTTAATACCAA
131 A-GGTCAGACTAAATGAATAAGTTATAACCTACATATTCCAATTATTTAATACCAA
* *
127042 TTATTTTATAACTAACGTTGTCATTGCAGGCCATCTACTCTCACTTGAACAATTCCAATTTTTTT
1 TTATTTTATAACTAACGTTGTCATTGAAAGCCATCTACTCTCACTTGAACAATTCCAA-TTTTTT
127107 CTTCATTTTTTGATACCTAATTTTTATATACAATTGAACCATCAACCAATTATTTAATATCAAAT
65 CTTCATTTTTTGATACCTAATTTTTATATACAATTGAACCATCAACCAATTATTTAATATCAAAT
127172 TAGGTCAGACTAAATGAATAAGTTATAACCTACATATT
130 TAGGTCAGACTAAATGAATAAGTTATAACCTACATATT
127210 GAAATAAGTT
Statistics
Matches: 156, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
185 56 0.36
186 100 0.64
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.42
Consensus pattern (185 bp):
TTATTTTATAACTAACGTTGTCATTGAAAGCCATCTACTCTCACTTGAACAATTCCAATTTTTTC
TTCATTTTTTGATACCTAATTTTTATATACAATTGAACCATCAACCAATTATTTAATATCAAATT
AGGTCAGACTAAATGAATAAGTTATAACCTACATATTCCAATTATTTAATACCAA
Found at i:130484 original size:5 final size:6
Alignment explanation
Indices: 130468--130492 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
130458 AATTTAACAA
130468 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
130493 AAACGGGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:142933 original size:36 final size:36
Alignment explanation
Indices: 142886--142959 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
142876 AGATCGGACG
142886 GAAGGAATTGATTAAACTACGTGAGGTCTATAAAAT
1 GAAGGAATTGATTAAACTACGTGAGGTCTATAAAAT
142922 GAAGGAATTGATTAAACTACGTGAGGTCTATAAAAT
1 GAAGGAATTGATTAAACTACGTGAGGTCTATAAAAT
142958 GA
1 GA
142960 CCAAAATACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (36 bp):
GAAGGAATTGATTAAACTACGTGAGGTCTATAAAAT
Found at i:146031 original size:4 final size:4
Alignment explanation
Indices: 146022--146057 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
146012 TCTTTTCTTT
*
146022 TCCC TCCC TCCC TTCC TCCC TCCC TCCC TCCC TCCC
1 TCCC TCCC TCCC TCCC TCCC TCCC TCCC TCCC TCCC
146058 ATTGAACTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.00, C:0.72, G:0.00, T:0.28
Consensus pattern (4 bp):
TCCC
Found at i:150840 original size:23 final size:23
Alignment explanation
Indices: 150814--150858 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
150804 ATTATGTAAA
*
150814 ATTTTAAATGTA-TATTATTTTAT
1 ATTTTAAATATATTA-TATTTTAT
*
150837 ATTTTTAATATATTATATTTTA
1 ATTTTAAATATATTATATTTTA
150859 AAAAATACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (23 bp):
ATTTTAAATATATTATATTTTAT
Found at i:154576 original size:17 final size:17
Alignment explanation
Indices: 154554--154587 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
154544 TGACTTTGAC
154554 CTGAAAAGTTAAATTTT
1 CTGAAAAGTTAAATTTT
*
154571 CTGAAAAGTTATATTTT
1 CTGAAAAGTTAAATTTT
154588 ATGTTTTTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (17 bp):
CTGAAAAGTTAAATTTT
Found at i:164565 original size:43 final size:43
Alignment explanation
Indices: 164518--164728 Score: 162
Period size: 42 Copynumber: 4.8 Consensus size: 43
164508 TTTCATTTTC
* * *
164518 ATTTTATTTAATTTTA-TTTTTATATTTATAATTGATGTTCTTA
1 ATTTT-TTTAATCTTACTTTTTATATTTATAATTGATGATCCTA
* ** * *
164561 ATTTTTGTAATCACACTTTTTTTATTTTTATAATTG-T-ATCATTA
1 ATTTTTTTAATCTTAC--TTTTTATATTTATAATTGATGATC-CTA
* * * *
164605 ATTTTTTCAATCTCATTTTTATATATTTATAATTGATGACCCTA
1 ATTTTTTTAATCTTACTTTT-TATATTTATAATTGATGATCCTA
* *
164649 ATTTTTTTTTCAATCTCACTTTTTA-ACTTTATAATTGA-GCTCCTA
1 A--TTTTTTT-AATCTTACTTTTTATA-TTTATAATTGATGATCCTA
**
164694 ATTTTTTTAATCTTACTTTTTACCTTTATAATTGA
1 ATTTTTTTAATCTTACTTTTTATATTTATAATTGA
164729 GACCCCTAAT
Statistics
Matches: 137, Mismatches: 19, Indels: 25
0.76 0.10 0.14
Matches are distributed among these distances:
42 34 0.25
43 27 0.20
44 20 0.15
45 26 0.19
46 19 0.14
47 11 0.08
ACGTcount: A:0.27, C:0.11, G:0.04, T:0.58
Consensus pattern (43 bp):
ATTTTTTTAATCTTACTTTTTATATTTATAATTGATGATCCTA
Found at i:164595 original size:45 final size:45
Alignment explanation
Indices: 164534--164643 Score: 138
Period size: 43 Copynumber: 2.5 Consensus size: 45
164524 TTTAATTTTA
*
164534 TTTTTATATTTATAATTGATGTTC-TTAATTTTTGT-AATCACACTT
1 TTTTTATATTTATAATTGATGATCATTAATTTTT-TCAATCACA-TT
* *
164579 TTTTTATTTTTATAATTG-T-ATCATTAATTTTTTCAATCTCATT
1 TTTTTATATTTATAATTGATGATCATTAATTTTTTCAATCACATT
*
164622 TTTATATATTTATAATTGATGA
1 TTTTTATATTTATAATTGATGA
164644 CCCTAATTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
43 21 0.38
44 17 0.30
45 18 0.32
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.59
Consensus pattern (45 bp):
TTTTTATATTTATAATTGATGATCATTAATTTTTTCAATCACATT
Found at i:164608 original size:44 final size:44
Alignment explanation
Indices: 164534--164655 Score: 142
Period size: 44 Copynumber: 2.8 Consensus size: 44
164524 TTTAATTTTA
*
164534 TTTTTATATTTATAATTGATGTTCTTAATTTTTGT-AATCACACTT
1 TTTTTATATTTATAATTGATGATCTTAATTTTT-TCAATCACA-TT
* *
164579 TTTTTATTTTTATAATTG-T-ATCATTAATTTTTTCAATCTCATT
1 TTTTTATATTTATAATTGATGATC-TTAATTTTTTCAATCACATT
* * *
164622 TTTATATATTTATAATTGATGACCCTAATTTTTT
1 TTTTTATATTTATAATTGATGATCTTAATTTTTT
164656 TTTCAATCTC
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
43 21 0.32
44 26 0.39
45 19 0.29
ACGTcount: A:0.27, C:0.09, G:0.05, T:0.59
Consensus pattern (44 bp):
TTTTTATATTTATAATTGATGATCTTAATTTTTTCAATCACATT
Found at i:164712 original size:42 final size:42
Alignment explanation
Indices: 164603--164775 Score: 158
Period size: 42 Copynumber: 4.0 Consensus size: 42
164593 ATTGTATCAT
* *
164603 TAATTTTTTCAATCTCA-TTTTTATATATTTATAATTGATGACCC
1 TAATTTTTTTAATCTCACTTTTTA-A-CTTTATAATTGA-GACCC
164647 TAATTTTTTTTTCAATCTCACTTTTTAACTTTATAATTGAG-CTCC
1 TAA--TTTTTTT-AATCTCACTTTTTAACTTTATAATTGAGAC-CC
* *
164692 TAATTTTTTTAATCTTACTTTTTACCTTTATAATTGAGACCCC
1 TAATTTTTTTAATCTCACTTTTTAACTTTATAATTGAGA-CCC
* * * * *
164735 TAA-TCTTTT-A-CTCACTTTTTACCTTTAAAATCGAGGCCC
1 TAATTTTTTTAATCTCACTTTTTAACTTTATAATTGAGACCC
164774 TA
1 TA
164776 CTTCAATCAT
Statistics
Matches: 113, Mismatches: 9, Indels: 19
0.80 0.06 0.13
Matches are distributed among these distances:
39 5 0.04
40 22 0.19
41 1 0.01
42 31 0.27
43 12 0.11
44 5 0.04
45 6 0.05
46 17 0.15
47 8 0.07
48 6 0.05
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50
Consensus pattern (42 bp):
TAATTTTTTTAATCTCACTTTTTAACTTTATAATTGAGACCC
Found at i:165074 original size:507 final size:504
Alignment explanation
Indices: 164440--165399 Score: 1329
Period size: 507 Copynumber: 1.9 Consensus size: 504
164430 TGGCTAGGTT
*
164440 GCTCAGGGGGCCCTTTTTTATAGGGTTACTATTTTTTTATTATATTTTTTATTTTTATAATTGAG
1 GCTCAGGGGG-CCTTTTTTATAGGGCTACTATTTTTTTATTATA--TTTTATTTTTATAATTGAG
** * *
164505 TATTTTCATTTTCATTTTATTTAATTTTATTTTTATATTTATAATTGATGTTCTTAATTTTTGTA
63 TATTTTCATTTTCATTCAATTTAATTTTATTTTTATATTTATAATTGATGTCCCTAATTTTTGTA
* * * *
164570 ATCACACTTTTTTTATTTTTATAATTG-TATCATTAATTTTTTCAATCTCATTTTTATATATTTA
128 ATCACAC--TTTTTATTTTTATAATTGAGACCATTAATTTTTTCAATCTCACTTTT-TACATTTA
164634 TAATTGATGAC-CCTAATTTTTTTTTCAATCTCACTTTTTA-ACTTTATAATTGA-GCTCCTAAT
190 TAATTGA--ACTCCTAA---TTTTTT-AATCTCACTTTTTACA-TTTATAATTGAGGC-CCTAAT
* * * *
164696 TTTTTTAATCTTACTTTTTACCTTTATAATTGAGACCCCTAA-TCTTTT-A-CTCACTTTTTACC
247 TTTTTTAATATCACTTTTGACCTTTAAAATTGAG-CCCCTAATTCTTTTAATCTCACTTTTTACC
*
164758 TTTAAAATCGAGG-CCCT-A-CTTCAATCATACTTTTTACTTTATAATTTAAATCCCTAATTTAA
311 TTTAAAATCGAGGTCCCTAATCTTCAATCATACTTTTTACTTTATAATTTAAACCCCTAATTTAA
164820 TAATTTTTATACGATTTATTAACGTAATTTTAAATTAATTATTCAAATTAATAGAATATACTTTC
376 TAA-TTTTATACGATTTATTAACGTAATTTTAAATTAATTATTC--A--AATAGAATATACTTTC
164885 AATTTATAAGGGCATAAGAAAACAAACGGTGTAACTAGGGCCGGCTATTAGGGTGCACTCTGAGC
436 AATTTATAAGGGCATAAGAAAACAAACGGTGTAACTAGGGCCGGCTATTAGGGTGCACTCTGAGC
164950 AATC
501 AATC
* * *
164954 GCTCAGGGGG-CTTTTTTTTAGGGCTCCTA-TTTTTTATTATA-TTT-TTTTTATAATTGAGTCT
1 GCTCAGGGGGCCTTTTTTATAGGGCTACTATTTTTTTATTATATTTTATTTTTATAATTGAGTAT
*
165015 TTTCATTTTC-TTCAATTTTATTTTTATTTTTATATTTATAATTGATGTCCCTAATTTTTGTAAT
66 TTTCATTTTCATTCAA-TTTAATTTTATTTTTATATTTATAATTGATGTCCCTAATTTTTGTAAT
*
165079 TACACTTTTTATTTTTATAATTGAGACCATTAATTTTTTCAATCTCACTTTTTACATTTATAATT
130 CACACTTTTTATTTTTATAATTGAGACCATTAATTTTTTCAATCTCACTTTTTACATTTATAATT
* *
165144 GAACTTCTAATTTTTTAATCTTACTTTTTACATTTATAATTGAGGCCCTAATTTTTTTAATATCA
195 GAACTCCTAATTTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCTAATTTTTTTAATATCA
** * *
165209 CTTTTGACCTTTAAAATTGAGGTCCTAATTTTTTTAATCTCACTTTTTACCTTTAAAATTGAGGT
260 CTTTTGACCTTTAAAATTGAGCCCCTAATTCTTTTAATCTCACTTTTTACCTTTAAAATCGAGGT
* * *
165274 CCTTAATTTTTTTCAATCATACTTTTTACTTTATAATTTAAACCCCTAATTTAATCATTTTATAC
325 CCCTAA---TCTTCAATCATACTTTTTACTTTATAATTTAAACCCCTAATTTAATAATTTTATAC
* *
165339 GATTTATTGACGTAATTTTAAATTAGTTATTCAAATAGAATATACTTTCAATTTATAAGGG
387 GATTTATTAACGTAATTTTAAATTAATTATTCAAATAGAATATACTTTCAATTTATAAGGG
165400 TATATCTTTT
Statistics
Matches: 402, Mismatches: 30, Indels: 39
0.85 0.06 0.08
Matches are distributed among these distances:
499 5 0.01
500 65 0.16
501 10 0.02
502 25 0.06
503 33 0.08
504 5 0.01
505 33 0.08
506 28 0.07
507 113 0.28
508 47 0.12
511 12 0.03
512 16 0.04
514 10 0.02
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.50
Consensus pattern (504 bp):
GCTCAGGGGGCCTTTTTTATAGGGCTACTATTTTTTTATTATATTTTATTTTTATAATTGAGTAT
TTTCATTTTCATTCAATTTAATTTTATTTTTATATTTATAATTGATGTCCCTAATTTTTGTAATC
ACACTTTTTATTTTTATAATTGAGACCATTAATTTTTTCAATCTCACTTTTTACATTTATAATTG
AACTCCTAATTTTTTAATCTCACTTTTTACATTTATAATTGAGGCCCTAATTTTTTTAATATCAC
TTTTGACCTTTAAAATTGAGCCCCTAATTCTTTTAATCTCACTTTTTACCTTTAAAATCGAGGTC
CCTAATCTTCAATCATACTTTTTACTTTATAATTTAAACCCCTAATTTAATAATTTTATACGATT
TATTAACGTAATTTTAAATTAATTATTCAAATAGAATATACTTTCAATTTATAAGGGCATAAGAA
AACAAACGGTGTAACTAGGGCCGGCTATTAGGGTGCACTCTGAGCAATC
Found at i:165149 original size:21 final size:21
Alignment explanation
Indices: 165125--165186 Score: 58
Period size: 20 Copynumber: 3.0 Consensus size: 21
165115 TTTCAATCTC
165125 ACTTTTTACATTTATAATTGA
1 ACTTTTTACATTTATAATTGA
* * *
165146 AC-TTCTA-ATTTTTTAATCT-T
1 ACTTTTTACA-TTTATAAT-TGA
165166 ACTTTTTACATTTATAATTGA
1 ACTTTTTACATTTATAATTGA
165187 GGCCCTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 10
0.65 0.13 0.22
Matches are distributed among these distances:
19 1 0.03
20 14 0.47
21 14 0.47
22 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.03, T:0.55
Consensus pattern (21 bp):
ACTTTTTACATTTATAATTGA
Found at i:165200 original size:42 final size:42
Alignment explanation
Indices: 165041--165311 Score: 273
Period size: 42 Copynumber: 6.4 Consensus size: 42
165031 TTTATTTTTA
* * *
165041 TTTTTATATTTATAATTGATGTCCCTAATTTTTGTAAT-TACAC
1 TTTTTACATTTATAATTGA-GGCCCTAATTTTTTTAATCT-CAC
** * * *
165084 TTTTTATTTTTATAATTGAGACCATTAATTTTTTCAATCTCAC
1 TTTTTACATTTATAATTGAGGCC-CTAATTTTTTTAATCTCAC
* * *
165127 TTTTTACATTTATAATTGA-ACTTCTAA-TTTTTTAATCTTAC
1 TTTTTACATTTATAATTGAGGC-CCTAATTTTTTTAATCTCAC
*
165168 TTTTTACATTTATAATTGAGGCCCTAATTTTTTTAATATCAC
1 TTTTTACATTTATAATTGAGGCCCTAATTTTTTTAATCTCAC
* * * *
165210 TTTTGACCTTTAAAATTGAGGTCCTAATTTTTTTAATCTCAC
1 TTTTTACATTTATAATTGAGGCCCTAATTTTTTTAATCTCAC
* * *
165252 TTTTTACCTTTAAAATTGAGGTCCTTAATTTTTTTCAATCAT-AC
1 TTTTTACATTTATAATTGAGG-CCCTAATTTTTTT-AATC-TCAC
165296 TTTTTAC-TTTATAATT
1 TTTTTACATTTATAATT
165312 TAAACCCCTA
Statistics
Matches: 196, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
41 35 0.18
42 78 0.40
43 68 0.35
44 14 0.07
45 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.06, T:0.53
Consensus pattern (42 bp):
TTTTTACATTTATAATTGAGGCCCTAATTTTTTTAATCTCAC
Found at i:166648 original size:29 final size:29
Alignment explanation
Indices: 166613--166694 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
166603 AAACTAAATT
** *
166613 GATGTCATTATTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
166642 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
166671 GATGTTATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
166695 GTTAGGTGAG
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 42 0.89
30 5 0.11
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:170804 original size:29 final size:29
Alignment explanation
Indices: 170769--170850 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
170759 AAACTAAATT
* *
170769 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
170798 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
170827 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
170851 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:173218 original size:35 final size:35
Alignment explanation
Indices: 173163--173274 Score: 125
Period size: 35 Copynumber: 3.2 Consensus size: 35
173153 TCTAAACCTT
** * *
173163 AAATTGAAGAATTTTAGAATTTGGGGTTTAAAATT
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * * *
173198 TAATTGAATTGTTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
* * *
173233 AAATTGAATTACTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
173268 AAATTGA
1 AAATTGA
173275 GGACTGTTTT
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 64 1.00
ACGTcount: A:0.36, C:0.01, G:0.23, T:0.40
Consensus pattern (35 bp):
AAATTGAATTATTTTGGAATTTGGGGTTTAAAATG
Found at i:182867 original size:18 final size:18
Alignment explanation
Indices: 182844--182878 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
182834 GAACAAAAAG
182844 AACTTAAACAA-ACCAAAC
1 AACTTAAA-AATACCAAAC
182862 AACTTAAAAATACCAAA
1 AACTTAAAAATACCAAA
182879 AAGAAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.63, C:0.23, G:0.00, T:0.14
Consensus pattern (18 bp):
AACTTAAAAATACCAAAC
Found at i:184087 original size:18 final size:17
Alignment explanation
Indices: 184056--184089 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
184046 TTAGAAAATA
*
184056 ATATCACGTCAACAATG
1 ATATCACGTAAACAATG
184073 ATATACACGTAAACAAT
1 ATAT-CACGTAAACAAT
184090 CAACACCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.21, G:0.09, T:0.24
Consensus pattern (17 bp):
ATATCACGTAAACAATG
Found at i:184515 original size:182 final size:181
Alignment explanation
Indices: 184302--184866 Score: 893
Period size: 182 Copynumber: 3.1 Consensus size: 181
184292 CGATACAAAT
* * * *
184302 AAAAAATGTATCGATC-CATAGCAAAATAACAGGTAAAAATATGACAAAATCGGTCTCAAAATGA
1 AAAAAATGTATCGA-CACTTAACAATATAACAGGTAAAAATATGATAAAA-CGGTCTCAAAATGA
* *
184366 CCAAACCGGTAAAGCGATACCGGATATGTTGAAAGTGTTGATACTTTATTATAAGTATCGACACT
64 CAAAACCGGTAAAGCGATACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACT
184431 TTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
129 TTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
*
184484 AAAAAATGTATCGACACTTAATAATATAACAGGTAAAAATATGATAAAACCGGTCTCAAAATGAC
1 AAAAAATGTATCGACACTTAACAATATAACAGGTAAAAATATGATAAAA-CGGTCTCAAAATGAC
* ** *
184549 AAAACCGATAAA-TAACTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTGTCGACACT
65 AAAACCGGTAAAGCGA-TACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACT
*
184613 TTTGGAATTTAAAAGACAAGCAGTAATAGCACCTATAAAGTGTCGATACTTTA
129 TTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
*
184666 AAAAAATATATCGACACTTAACAATATAACAGGTAAAAATATGATAAAACTGGTCTCAAAATGAC
1 AAAAAATGTATCGACACTTAACAATATAACAGGTAAAAATATGATAAAAC-GGTCTCAAAATGAC
**
184731 AAAACCGGTAAAGCGCCACCGGATATGTT-AAATGTGTCGATACTTTATTATAAGTATCGACACT
65 AAAACCGGTAAAGCGATACCGGATATGTTGAAA-GTGTCGATACTTTATTATAAGTATCGACACT
* * *
184795 TTTGGAATTTAAAAGACAAGCAGTAATAGTGCGTATAAAGTGTTGATACTTTA
129 TTTGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
184848 AAAAAATGTATCGACACTT
1 AAAAAATGTATCGACACTT
184867 GGGTTATTGT
Statistics
Matches: 352, Mismatches: 26, Indels: 10
0.91 0.07 0.03
Matches are distributed among these distances:
181 6 0.02
182 346 0.98
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (181 bp):
AAAAAATGTATCGACACTTAACAATATAACAGGTAAAAATATGATAAAACGGTCTCAAAATGACA
AAACCGGTAAAGCGATACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGTATCGACACTTT
TGGAATTTAAAAGACAAGCAGTAATAGCGCCTATAAAGTGTCGATACTTTA
Found at i:187193 original size:19 final size:19
Alignment explanation
Indices: 187169--187216 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
187159 TTACATCCAC
187169 ATACAAAATTA-GAAATCGT
1 ATACAAAATTACG-AATCGT
*
187188 ATACAAAATTACGAATTGT
1 ATACAAAATTACGAATCGT
187207 ATACAAAATT
1 ATACAAAATT
187217 TCCCCTACAT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 26 0.96
20 1 0.04
ACGTcount: A:0.52, C:0.10, G:0.08, T:0.29
Consensus pattern (19 bp):
ATACAAAATTACGAATCGT
Found at i:189602 original size:199 final size:199
Alignment explanation
Indices: 189149--190136 Score: 1331
Period size: 199 Copynumber: 5.0 Consensus size: 199
189139 GCGTAATTTT
* * * *
189149 AAAAAGTATCGACACAACTTTAAAAAATTTCGATACTTTATGTATACCTATTTTCTAATTAACTG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACTTTATGTAGACCTATTTTCTAATTAACCG
189214 GTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCG-ATTTCGATGTTT
66 GTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTA-TTCGATGTTT
* ** * * * *
189278 TTGGGATTGATACAATTT-TAAATGTATCAAAACTTTAAGTGTGCACCTCGTTGGGCATTCATTC
130 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
189342 TGGTC
195 TGGTC
* **
189347 AAAACGTATCGACACAACTTTAAATGGTGTCGATACTTTATGTAGACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACTTTATGTAGACCTATTTTCTAATTAACCG
* *
189412 GTATATTTTTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTATTCAATGTTTT
66 GTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTATTCGATGTTTT
* * *
189477 TGGGATCGATACGTTTTATAAATGTATCGACACTTTATGCGTACAACTCGTTGGGCATTCATTCT
131 TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
189542 GGTC
196 GGTC
* * *
189546 AAAAAGGATCGACACAACTTTAAAAAGTGTCGATACCTTATGTAGACATATTTTCTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACTTTATGTAGACCTATTTTCTAATTAACCG
* * * *
189611 GTATATTTCTACTGGTTACATTGTAAAGTTATCTATTACATTATAATTATC-AATTTTGAT-TTT
66 GTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTA-TTCGATGTTT
* * ** * *
189674 TTGGTATCCATAC-AATTGTAAATGTATCGACAATTTATGCGTGCACCTCGTTGGGCATTCATTC
130 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
189738 TGGTC
195 TGGTC
* * * *
189743 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTATGTATACCTATTTTCTAATTAATCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACTTTATGTAGACCTATTTTCTAATTAACCG
* * * * * *
189808 GTATATTTCTACTGGTTACATTGGAAATTTACTTATTACATTATATTTATCGTATTCTATGTTTT
66 GTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTATTCGATGTTTT
* * * *
189873 TAGGATCGATACTTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGTTGGGCTTTCATTT
131 TGGGATCGATAC-TTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTC
189938 TGGTC
195 TGGTC
* ** * * * ** *
189943 AAAACGTATTAACACAAATTTAAAAAGTGTTGATACATTATACAGACCTATTTTTTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACTTTATGTAGACCTATTTTCTAATTAACCG
* * * *
190008 GTATATTTCTATCGGTTACATTGGAAA-TTGACCTATTACATTATAATTATCTTATTTGATGTTT
66 GTATATTTCTACCGGTTACATTGTAAAGTT-ACCTATTACATTATAATTATCGTATTCGATGTTT
* * *
190072 TTGGGATCAATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCATT
130 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTC-GTTGGGCATTCATT
190137 ATGGAGATTA
Statistics
Matches: 696, Mismatches: 85, Indels: 16
0.87 0.11 0.02
Matches are distributed among these distances:
197 158 0.23
198 162 0.23
199 196 0.28
200 180 0.26
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (199 bp):
AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACTTTATGTAGACCTATTTTCTAATTAACCG
GTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTATTCGATGTTTT
TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCT
GGTC
Found at i:189944 original size:397 final size:396
Alignment explanation
Indices: 189149--190136 Score: 1363
Period size: 397 Copynumber: 2.5 Consensus size: 396
189139 GCGTAATTTT
* * * * *
189149 AAAAAGTATCGACACAACTTTAAAAAATTTCGATACTTTATGTATACCTATTTTCTAATTAACTG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* *
189214 GTATATTTCTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGATTTCGATGTTTT
66 GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATC-ATTTTGATGTTTT
** * * * *
189279 TGGGATTGATACAATTTTAAATGTATC-AAAACTTTAAGTGTGCACCTCGTTGGGCATTCATTCT
130 TGGGATCAATACAATTATAAATGTATCGACAA-TTTATGCGTGCACCTCGTTGGGCATTCATTCT
* * ** *
189343 GGTCAAAACGTATCGACACAACTTTAAATGGTGTCGATACTTTATGTAGACCTATTTTCTAATTA
194 GGTCAAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTATGTAGACCTATTTTCTAATTA
* *
189408 ACCGGTATATTTTTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTATTCAATG
259 ACCGGTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGTATTCAATG
*
189473 TTTTTGGGATCGATACGTTTTATAAATGTATCGACACTTTATGCGTACAACTCGTTGGGCATTCA
324 TTTTTAGGATCGATACGTTTTATAAATGTATCGACACTTTATGCGTACAACTCGTTGGGCATTCA
189538 TTCTGGTC
389 TTCTGGTC
* * *
189546 AAAAAGGATCGACACAACTTTAAAAAGTGTCGATACCTTATGTAGACATATTTTCTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
*
189611 GTATATTTCTACTGGTTACATTGTAAAGTTATCTATTACATTATAATTATCAATTTTGAT-TTTT
66 GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATC-ATTTTGATGTTTT
* * *
189675 TGGTATCCATACAATTGTAAATGTATCGACAATTTATGCGTGCACCTCGTTGGGCATTCATTCTG
130 TGGGATCAATACAATTATAAATGTATCGACAATTTATGCGTGCACCTCGTTGGGCATTCATTCTG
*
189740 GTCAAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTATGTATACCTATTTTCTAATTAA
195 GTCAAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTATGTAGACCTATTTTCTAATTAA
* * * * * *
189805 TCGGTATATTTCTACTGGTTACATTGGAAATTTACTTATTACATTATATTTATCGTATTCTATGT
260 CCGGTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGTATTCAATGT
* * * * *
189870 TTTTAGGATCGATACTTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGTTGGGCTTTCA
325 TTTTAGGATCGATAC-GTTTTATAAATGTATCGACACTTTATGCGTACAACTCGTTGGGCATTCA
*
189935 TTTTGGTC
389 TTCTGGTC
* ** * * ** *
189943 AAAACGTATTAACACAAATTTAAAAAGTGTTGATACATTATACAGACCTATTTTTTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
* *
190008 GTATATTTCTA-TCGGTTACATTGGAAA-TTGACCTATTACATTATAATTATCTTATTTGATGTT
66 GTATATTTCTACT-GGTTACATTGTAAAGTT-ACCTATTACATTATAATTATCAT-TTTGATGTT
** * * *
190071 TTTGGGATCAATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCGGTTGGTCATTCAT
128 TTTGGGATCAATAC-AATTATAAATGTATCGACAATTTATGCGTGCACCTC-GTTGGGCATTCAT
190136 T
191 T
190137 ATGGAGATTA
Statistics
Matches: 522, Mismatches: 61, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
396 192 0.37
397 272 0.52
398 14 0.03
399 31 0.06
400 13 0.02
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (396 bp):
AAAAAGTATCGACACAACTTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAACCG
GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATCATTTTGATGTTTTT
GGGATCAATACAATTATAAATGTATCGACAATTTATGCGTGCACCTCGTTGGGCATTCATTCTGG
TCAAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTATGTAGACCTATTTTCTAATTAAC
CGGTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGTATTCAATGTT
TTTAGGATCGATACGTTTTATAAATGTATCGACACTTTATGCGTACAACTCGTTGGGCATTCATT
CTGGTC
Found at i:192869 original size:3 final size:3
Alignment explanation
Indices: 192861--192899 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
192851 ACTTGTTTGG
*
192861 ATC ATC ATC ATC ATC ATC ATC TTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
192900 TTTATTGACC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.31, C:0.33, G:0.00, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:193512 original size:23 final size:23
Alignment explanation
Indices: 193462--193506 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
193452 TGCCTATTTT
*
193462 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
193485 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
193507 TGTTATTGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:196169 original size:199 final size:199
Alignment explanation
Indices: 195709--196696 Score: 1391
Period size: 199 Copynumber: 5.0 Consensus size: 199
195699 GCGTAATTTT
* *
195709 AAAAAGTATCGACACAACTTTAAAAAATGTTGATACTTTATGTATACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTTGATACTTTATGTAGACCTATTTTCTAATTAACCG
*
195774 GTATATTTCTACTGATTACATTGTAAAGTTACCTATTACATTATAATTATCAGT-TTCGATGTTT
66 GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATC-GTATTCGATGTTT
** * *
195838 TTGGGATCGATACAATTT-TAAATGTATCGACACTTTAAGCGTGCACCTCGTTGGGCATTCATTC
130 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTC
195902 TGGTC
195 TGGTC
*
195907 AAAACGTATCGACACAACTTTAAAAAGTGTTGATACTTTATGTAGACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTTGATACTTTATGTAGACCTATTTTCTAATTAACCG
* *
195972 GTATATTTTTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTATTCGATGTTTT
66 GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTATTCGATGTTTT
* * *
196037 TGGGATCGATACGTTTTATAAATGTATC-AGCACTTTATGTGTGCAACTCGTTGGACATTCATTC
131 TGGGATCGATACTTTTTATAAATGTATCGA-CACTTTATGTGTGCACCTCGTTGGGCATTCATTC
*
196101 TGGTA
195 TGGTC
* * * *
196106 AAAAAGGATCGATACAACTTTAAAAAGTGTTGATACCTTATGTAGACATATTTTCTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTTGATACTTTATGTAGACCTATTTTCTAATTAACCG
* *
196171 GTATATTTCTACTGGTTACATTGTAAAGTTATCTATTACATTATAATTATCG-ATTTTGAT-TTT
66 GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTA-TTCGATGTTT
* ** * * * *
196234 TTGGTATCGATAC-AATTGTAAATGTATCGACAATTTATGCGTGCACCTCGTAGGGCATTCATTC
130 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTC
196298 TGGTC
195 TGGTC
* * * * *
196303 AAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTATGTATACCTATTTTCTAATTAATCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTTGATACTTTATGTAGACCTATTTTCTAATTAACCG
* * * *
196368 GTATATTTCTACTGGTTACATTGGAAATTTACCTATTACATTATATTTATCGTATTCTATGTTTT
66 GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTATTCGATGTTTT
* * *
196433 TAGGATCGATACTTTTTTATAAATGTATCGACACTTTAT-TCGTGCACCTTGTTGGGCTTTCATT
131 TGGGATCGATAC-TTTTTATAAATGTATCGACACTTTATGT-GTGCACCTCGTTGGGCATTCATT
*
196497 TTGGTC
194 CTGGTC
* * * * * *
196503 AAAACGTATCAACACAATTTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAATCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTTGATACTTTATGTAGACCTATTTTCTAATTAACCG
* * *
196568 GTATATTTCTACCGGTTACATTGGAAA-TTGACCTATTACATTATAATTATCTTATTCGATGTTT
66 GTATATTTCTACTGGTTACATTGTAAAGTT-ACCTATTACATTATAATTATCGTATTCGATGTTT
*
196632 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTAT-TCGTGCACCTCTGTTGGTCATTCAT
130 TTGGGATCGATACTTTTTATAAATGTATCGACACTTTATGT-GTGCACCTC-GTTGGGCATTCAT
196696 T
193 T
196697 ATGGAGATTA
Statistics
Matches: 706, Mismatches: 72, Indels: 22
0.88 0.09 0.03
Matches are distributed among these distances:
197 155 0.22
198 169 0.24
199 196 0.28
200 186 0.26
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (199 bp):
AAAAAGTATCGACACAACTTTAAAAAGTGTTGATACTTTATGTAGACCTATTTTCTAATTAACCG
GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTATTCGATGTTTT
TGGGATCGATACTTTTTATAAATGTATCGACACTTTATGTGTGCACCTCGTTGGGCATTCATTCT
GGTC
Found at i:196575 original size:397 final size:396
Alignment explanation
Indices: 195709--196696 Score: 1428
Period size: 397 Copynumber: 2.5 Consensus size: 396
195699 GCGTAATTTT
* * *
195709 AAAAAGTATCGACACAACTTTAAAAAATGTTGATACTTTATGTATACCTATTTTCTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTTGATACATTATGTAGACCTATTTTCTAATTAACCG
* *
195774 GTATATTTCTACTGATTACATTGTAAAGTTACCTATTACATTATAATTATCAGTTTCGATGTTTT
66 GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATCA-TTTTGATGTTTT
* *
195839 TGGGATCGATACAATTTTAAATGTATCGACACTTTAAGCGTGCACCTCGTTGGGCATTCATTCTG
130 TGGGATCGATACAATTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTG
* * * *
195904 GTCAAAACGTATCGACACAACTTTAAAAAGTGTTGATACTTTATGTAGACCTATTTTCTAATTAA
195 GTCAAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTATGTAGACCTATTTTCTAATTAA
* *
195969 CCGGTATATTTTTACCGGTTACATTGTAAAGTTACCTATTACATTATAATTATCGTATTCGATGT
260 CCGGTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGTATTCGATGT
*
196034 TTTTGGGATCGATACGTTTTATAAATGTATCAGCACTTTATGTGTGCAACTCGTTGGACATTCAT
325 TTTTAGGATCGATACGTTTTATAAATGTATCAGCACTTTATGTGTGCAACTCGTTGGACATTCAT
196099 TCTGGTA
390 TCTGGTA
* * * *
196106 AAAAAGGATCGATACAACTTTAAAAAGTGTTGATACCTTATGTAGACATATTTTCTAATTAACCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTTGATACATTATGTAGACCTATTTTCTAATTAACCG
*
196171 GTATATTTCTACTGGTTACATTGTAAAGTTATCTATTACATTATAATTATCGATTTTGAT-TTTT
66 GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATC-ATTTTGATGTTTT
* * * *
196235 TGGTATCGATACAATTGTAAATGTATCGACAATTTATGCGTGCACCTCGTAGGGCATTCATTCTG
130 TGGGATCGATACAATTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTG
*
196300 GTCAAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTATGTATACCTATTTTCTAATTAA
195 GTCAAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTATGTAGACCTATTTTCTAATTAA
* * * * *
196365 TCGGTATATTTCTACTGGTTACATTGGAAATTTACCTATTACATTATATTTATCGTATTCTATGT
260 CCGGTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGTATTCGATGT
* * * * *
196430 TTTTAGGATCGATACTTTTTTATAAATGTATC-GACACTTTAT-TCGTGCACCTTGTTGGGCTTT
325 TTTTAGGATCGATAC-GTTTTATAAATGTATCAG-CACTTTATGT-GTGCAACTCGTTGGACATT
* *
196493 CATTTTGGTC
387 CATTCTGGTA
* * * * *
196503 AAAACGTATCAACACAATTTTAAAAAGTGTCGATACATTATGTAGACCTATTTTCTAATTAATCG
1 AAAAAGTATCGACACAACTTTAAAAAGTGTTGATACATTATGTAGACCTATTTTCTAATTAACCG
* *
196568 GTATATTTCTACCGGTTACATTGGAAA-TTGACCTATTACATTATAATTATC-TTATTCGATGTT
66 GTATATTTCTACTGGTTACATTGTAAAGTT-ACCTATTACATTATAATTATCATT-TT-GATGTT
** * *
196631 TTTGGGATCGATACTTTTTATAAATGTATCGACACTTTATTCGTGCACCTCTGTTGGTCATTCAT
128 TTTGGGATCGATAC-AATTATAAATGTATCGACACTTTATGCGTGCACCTC-GTTGGGCATTCAT
196696 T
191 T
196697 ATGGAGATTA
Statistics
Matches: 527, Mismatches: 54, Indels: 17
0.88 0.09 0.03
Matches are distributed among these distances:
395 2 0.00
396 202 0.38
397 264 0.50
398 16 0.03
399 31 0.06
400 12 0.02
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.40
Consensus pattern (396 bp):
AAAAAGTATCGACACAACTTTAAAAAGTGTTGATACATTATGTAGACCTATTTTCTAATTAACCG
GTATATTTCTACTGGTTACATTGTAAAGTTACCTATTACATTATAATTATCATTTTGATGTTTTT
GGGATCGATACAATTATAAATGTATCGACACTTTATGCGTGCACCTCGTTGGGCATTCATTCTGG
TCAAAAAGTATCGACACAAATTTAAAAAGTATCGATACTTTATGTAGACCTATTTTCTAATTAAC
CGGTATATTTCTACCGGTTACATTGGAAAGTTACCTATTACATTATAATTATCGTATTCGATGTT
TTTAGGATCGATACGTTTTATAAATGTATCAGCACTTTATGTGTGCAACTCGTTGGACATTCATT
CTGGTA
Found at i:200023 original size:23 final size:23
Alignment explanation
Indices: 199997--200055 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
199987 CGGTTAAATG
*
199997 CCTATTTTATTATATAAGCACTA
1 CCTATTATATTATATAAGCACTA
* *
200020 CCTATTACATTATATAAGCGCTA
1 CCTATTATATTATATAAGCACTA
*
200043 CCTAATATATTAT
1 CCTATTATATTAT
200056 TGTACTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.36, C:0.19, G:0.05, T:0.41
Consensus pattern (23 bp):
CCTATTATATTATATAAGCACTA
Found at i:205474 original size:31 final size:31
Alignment explanation
Indices: 205407--205466 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
205397 CAATTTAAGG
*
205407 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
205438 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
205467 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:206479 original size:31 final size:31
Alignment explanation
Indices: 206412--206471 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
206402 CAATTTAAGG
*
206412 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
206443 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
206472 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:206563 original size:19 final size:19
Alignment explanation
Indices: 206536--206572 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
206526 AATGTTTTTA
* *
206536 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
206555 TGAACAGTAAATTACTAT
1 TGAACAGTAAATTACTAT
206573 GAAGGGGTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:206994 original size:34 final size:32
Alignment explanation
Indices: 206955--207024 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 32
206945 TTTTGTAAAG
*
206955 GGGAAAGGTTCTAGTTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGTTTAGCCCG-G-AAAAACTA
206989 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
207021 GGGA
1 GGGA
207025 GTTGTAAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 11 0.31
33 1 0.03
34 23 0.66
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
Found at i:218498 original size:25 final size:23
Alignment explanation
Indices: 218444--218499 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 23
218434 TTTTGTTTTG
*
218444 AAAAATTATAAAATAAAATAAGA
1 AAAAATTAGAAAATAAAATAAGA
* *
218467 ATGAAATTAAGAAAATAATATAAGA
1 A-AAAATT-AGAAAATAAAATAAGA
218492 TAAAAATT
1 -AAAAATT
218500 TCATTATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.04
24 5 0.19
25 19 0.73
26 1 0.04
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (23 bp):
AAAAATTAGAAAATAAAATAAGA
Found at i:220439 original size:25 final size:24
Alignment explanation
Indices: 220392--220444 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
220382 CCAACCCACC
*
220392 CTAAAAGTTTATAAATTCATCCCT
1 CTAAAAGTTTAGAAATTCATCCCT
* **
220416 ACTAAAATTTTAGAAATTTGTCCCT
1 -CTAAAAGTTTAGAAATTCATCCCT
220441 CTAA
1 CTAA
220445 CATAAGATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (24 bp):
CTAAAAGTTTAGAAATTCATCCCT
Found at i:221962 original size:21 final size:21
Alignment explanation
Indices: 221936--221982 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
221926 CCTGTTCATG
221936 TTAACATCACATCTCTTAATA
1 TTAACATCACATCTCTTAATA
* ** *
221957 TTAACATTATGTCTCTTCATA
1 TTAACATCACATCTCTTAATA
221978 TTAAC
1 TTAAC
221983 GTAACATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.21, G:0.02, T:0.43
Consensus pattern (21 bp):
TTAACATCACATCTCTTAATA
Found at i:227422 original size:2 final size:2
Alignment explanation
Indices: 227415--227482 Score: 93
Period size: 2 Copynumber: 34.0 Consensus size: 2
227405 TAATTAATTG
* * *
227415 AT AT AT AT AT AT AG GT AT GT AT GA- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
227457 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
227483 TGTTATTTAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
1 1 0.02
2 56 0.97
3 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (2 bp):
AT
Found at i:230393 original size:7 final size:7
Alignment explanation
Indices: 230381--230444 Score: 101
Period size: 7 Copynumber: 8.7 Consensus size: 7
230371 TATAATGCAT
230381 GGCAGTA
1 GGCAGTA
230388 GGCAGTA
1 GGCAGTA
230395 GGCAGTA
1 GGCAGTA
230402 GGCAGTA
1 GGCAGTA
230409 GGCAGTA
1 GGCAGTA
230416 GGCAGTA
1 GGCAGTA
230423 GGCAGTAGTA
1 GGC---AGTA
230433 GGCAGTA
1 GGCAGTA
230440 GGCAG
1 GGCAG
230445 GCCTTTGCCT
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
7 47 0.87
10 7 0.13
ACGTcount: A:0.28, C:0.14, G:0.44, T:0.14
Consensus pattern (7 bp):
GGCAGTA
Found at i:234513 original size:143 final size:145
Alignment explanation
Indices: 234250--234521 Score: 476
Period size: 143 Copynumber: 1.9 Consensus size: 145
234240 ATATCAAATA
*
234250 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTTCAATCTTAAAAGAGTACACTTTTAA
1 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTACAATCTTAAAAGAGTACACTTTTAA
* *
234315 ACTAAGAAACTTGTATTCGTTGACACCTTACTGTAACATATCAACTAGTCATTGGACCGGTTGAT
66 ACTAAGAAACATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAT
234380 CCTATACTTTGAATC
131 CCTATACTTTGAATC
*
234395 TACAATTAAAATCAAGGAAAATG-AA-ACTATGAAAATTACAATCTTAAAAGAGTACACTTTTAA
1 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTACAATCTTAAAAGAGTACACTTTTAA
* *
234458 ACTAAGAAGCATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCCTTGGACCGGTTGA
66 ACTAAGAAACATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGA
234522 ACCTGCACTT
Statistics
Matches: 121, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
143 96 0.79
144 2 0.02
145 23 0.19
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (145 bp):
TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTACAATCTTAAAAGAGTACACTTTTAA
ACTAAGAAACATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAT
CCTATACTTTGAATC
Found at i:239288 original size:2 final size:2
Alignment explanation
Indices: 239277--239307 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
239267 TGTCGTTACA
239277 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
239308 TTCATTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:240637 original size:3 final size:3
Alignment explanation
Indices: 240631--240669 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
240621 ACAATGAGGT
* * *
240631 TCC TCC TTC TCC TTC TCC TCC TCC TCC TCC TTC TCC TCC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC
240670 ACATTTCCCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (3 bp):
TCC
Found at i:241013 original size:72 final size:72
Alignment explanation
Indices: 240913--241051 Score: 278
Period size: 72 Copynumber: 1.9 Consensus size: 72
240903 TTCCTCCAAA
240913 ACCTCTCCGTCGCAGCCAACCAGCTTTCCGGTCCAATCCCAATGGAACTCTCTGCCCTCTCCGGT
1 ACCTCTCCGTCGCAGCCAACCAGCTTTCCGGTCCAATCCCAATGGAACTCTCTGCCCTCTCCGGT
240978 CTGCGTG
66 CTGCGTG
240985 ACCTCTCCGTCGCAGCCAACCAGCTTTCCGGTCCAATCCCAATGGAACTCTCTGCCCTCTCCGGT
1 ACCTCTCCGTCGCAGCCAACCAGCTTTCCGGTCCAATCCCAATGGAACTCTCTGCCCTCTCCGGT
241050 CT
66 CT
241052 ATTTCATCTC
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.16, C:0.42, G:0.18, T:0.24
Consensus pattern (72 bp):
ACCTCTCCGTCGCAGCCAACCAGCTTTCCGGTCCAATCCCAATGGAACTCTCTGCCCTCTCCGGT
CTGCGTG
Found at i:242024 original size:143 final size:145
Alignment explanation
Indices: 241761--242045 Score: 475
Period size: 143 Copynumber: 2.0 Consensus size: 145
241751 ATATCAAATA
*
241761 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTTCAATCATAAAAGAGTTCACTTTTAA
1 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTTCAATCATAAAAGAGTACACTTTTAA
* *
241826 ACTAAGAAACTTGTATTCGTTGACACCTTACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
66 ACTAAGAAACATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
*
241891 CCTATACTTTGAATC
131 CCTACACTTTGAATC
* *
241906 TACAATTAAAATCAAGGAAAATG-AA-ACTATGAAAATTTCAATCTTAAAAGAGTACACTTTTAA
1 TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTTCAATCATAAAAGAGTACACTTTTAA
* *
241969 ACTAAGAAGCATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCCTTGGACCGGTTGAA
66 ACTAAGAAACATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
*
242034 CCTGCACTTTGA
131 CCTACACTTTGA
242046 TACCCCTAAA
Statistics
Matches: 131, Mismatches: 9, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
143 106 0.81
144 2 0.02
145 23 0.18
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (145 bp):
TACAATTAAAATCAAGGAAAATGAAACACTATCAAAATTTCAATCATAAAAGAGTACACTTTTAA
ACTAAGAAACATGTATTCGTTGACACCATACTGTAACATATCAACTAGTCATTGGACCGGTTGAA
CCTACACTTTGAATC
Found at i:249771 original size:52 final size:53
Alignment explanation
Indices: 249706--249812 Score: 162
Period size: 52 Copynumber: 2.0 Consensus size: 53
249696 CACAAGATGG
* * *
249706 GGCACATAGAAATAGGAAACTAGTCTAGAGTTAGGGGATTACAATTAATTACAA
1 GGCACATA-AAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACAA
*
249760 GGCACAT-AAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATCACAA
1 GGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACAA
249812 G
1 G
249813 AATATTATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
52 42 0.86
54 7 0.14
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.21
Consensus pattern (53 bp):
GGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACAA
Found at i:262918 original size:19 final size:18
Alignment explanation
Indices: 262894--262953 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
262884 AACTATTGTT
262894 TATATAAAGTTATAAACTA
1 TATATAAA-TTATAAACTA
* *
262913 TATATAAATTATCAACTG
1 TATATAAATTATAAACTA
* * *
262931 TCTATACA-TATATACTA
1 TATATAAATTATAAACTA
262948 TATATA
1 TATATA
262954 TTACTTATAT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
17 11 0.33
18 14 0.42
19 8 0.24
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (18 bp):
TATATAAATTATAAACTA
Found at i:263035 original size:25 final size:23
Alignment explanation
Indices: 263001--263126 Score: 89
Period size: 24 Copynumber: 5.2 Consensus size: 23
262991 TTAATATAAA
263001 TTAT-AATTTATAAACTATATATT
1 TTATAAATTTATAAA-TATATATT
*
263024 TTATAAAGTTTATACATATATATT
1 TTATAAA-TTTATAAATATATATT
*
263048 TTATATATATATATATATAA-ATATAAT
1 TTATA-A-AT-T-TATA-AATATATATT
263075 TTAT-AATTTATAAACTATATACTT
1 TTATAAATTTATAAA-TATATA-TT
* * *
263099 TT-TATAGTTTATACATATATAGT
1 TTATA-AATTTATAAATATATATT
263122 TTATA
1 TTATA
263127 TACATAGTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 25
0.72 0.06 0.22
Matches are distributed among these distances:
21 2 0.02
22 4 0.05
23 14 0.17
24 28 0.34
25 18 0.22
26 2 0.02
27 14 0.17
28 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
TTATAAATTTATAAATATATATT
Found at i:263059 original size:15 final size:15
Alignment explanation
Indices: 263032--263061 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
263022 TTTTATAAAG
263032 TTTATACATATATAT
1 TTTATACATATATAT
*
263047 TTTATATATATATAT
1 TTTATACATATATAT
263062 ATATAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTATACATATATAT
Found at i:263078 original size:51 final size:52
Alignment explanation
Indices: 263017--263119 Score: 122
Period size: 53 Copynumber: 2.0 Consensus size: 52
263007 TTTATAAACT
* * *
263017 ATATATTTTATAAAGTTTATACA-TATATA-TTTTATA-TATATATATATATAA
1 ATATAATTTAT-AA-TTTATAAACTATATACTTTTATAGTATATACATATATAA
*
263068 ATATAATTTATAATTTATAAACTATATACTTTTTATAGTTTATACATATATA
1 ATATAATTTATAATTTATAAACTATATAC-TTTTATAGTATATACATATATA
263120 GTTTATATAC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
49 7 0.16
50 8 0.18
51 10 0.23
52 7 0.16
53 12 0.27
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (52 bp):
ATATAATTTATAATTTATAAACTATATACTTTTATAGTATATACATATATAA
Found at i:263083 original size:74 final size:75
Alignment explanation
Indices: 262977--263128 Score: 245
Period size: 74 Copynumber: 2.0 Consensus size: 75
262967 TTATACATAC
*
262977 ATATATATACTATATTAATATAAATTATAATTTATAAACTATATA-TTTTATAAAGTTTATACAT
1 ATATATATACTATATAAATATAAATTATAATTTATAAACTATATACTTTT-TAAAGTTTATACAT
*
263041 ATATATTTTAT
65 ATATAGTTTAT
* *
263052 ATATATATA-TATATAAATATAATTTATAATTTATAAACTATATACTTTTTATAGTTTATACATA
1 ATATATATACTATATAAATATAAATTATAATTTATAAACTATATACTTTTTAAAGTTTATACATA
263116 TATAGTTTAT
66 TATAGTTTAT
263126 ATA
1 ATA
263129 CATAGTTTAT
Statistics
Matches: 72, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
74 59 0.82
75 13 0.18
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (75 bp):
ATATATATACTATATAAATATAAATTATAATTTATAAACTATATACTTTTTAAAGTTTATACATA
TATAGTTTAT
Found at i:263093 original size:27 final size:27
Alignment explanation
Indices: 263041--263093 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
263031 GTTTATACAT
* *
263041 ATATATTTTATATATATATATATATAA
1 ATATAATTTATATATATATAAATATAA
*
263068 ATATAATTTATA-ATTTATAAACTATA
1 ATATAATTTATATATATATAAA-TATA
263094 TACTTTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
ATATAATTTATATATATATAAATATAA
Found at i:263146 original size:13 final size:13
Alignment explanation
Indices: 263101--263148 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
263091 ATATACTTTT
263101 TATAGTTTATACATA
1 TATAGTTTAT--ATA
263116 TATAGTTTATATA
1 TATAGTTTATATA
* *
263129 CATAGTTTATATT
1 TATAGTTTATATA
263142 TATAGTT
1 TATAGTT
263149 GAGTTTTAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 20 0.67
15 10 0.33
ACGTcount: A:0.35, C:0.04, G:0.08, T:0.52
Consensus pattern (13 bp):
TATAGTTTATATA
Found at i:263493 original size:29 final size:29
Alignment explanation
Indices: 263451--263908 Score: 693
Period size: 29 Copynumber: 15.8 Consensus size: 29
263441 TTGTTTCCAC
*
263451 GGTATGCGAAGACTCTTGACGTGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
*
263480 GGTATGCGAAGACTCTTGACGTGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
*
263509 GGTATGCGAAGACTCTTGACGTGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
* *
263538 GGTATG-GAAAGACTCTTGACGTAGACTTG
1 GGTATGCG-AAGACTCCTGACGTGGACTTG
* *
263567 GGTATACGAAGACTCCTGACGAGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
*
263596 GGTATGCAAAGACTCCTGACGTGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
263625 GGTATGCGAAGACTCCTGACGTGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
*
263654 GGTATGCGAAGACTCCTGACGAGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
*
263683 AGTATGCGAAGACTCCTGACGTGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
* *
263712 GGTATGCGAAGACTCCTAACTTGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
* **
263741 GGTATGAGAAGACTCCTGACAAGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
* **
263770 GGTATGCAAAGACTCCTGATATGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
*
263799 GGTATGCGAAGACTCTTGACGTGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
* *
263828 GGTATTCGAAGACTCCTGACGTGAACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
*
263857 GGTATGCGAAGACTCTTGACGTGGACTTG
1 GGTATGCGAAGACTCCTGACGTGGACTTG
*
263886 GGTATGCGAAGACTCTTGACGTG
1 GGTATGCGAAGACTCCTGACGTG
263909 TTTTTCCCCT
Statistics
Matches: 394, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
28 1 0.00
29 392 0.99
30 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.26
Consensus pattern (29 bp):
GGTATGCGAAGACTCCTGACGTGGACTTG
Found at i:264394 original size:10 final size:10
Alignment explanation
Indices: 264379--264408 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
264369 GTAGACAGTC
264379 AAATCATGTT
1 AAATCATGTT
264389 AAATCATGTT
1 AAATCATGTT
264399 AAATCATGTT
1 AAATCATGTT
264409 TCTTACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (10 bp):
AAATCATGTT
Found at i:265173 original size:58 final size:58
Alignment explanation
Indices: 265083--265198 Score: 187
Period size: 58 Copynumber: 2.0 Consensus size: 58
265073 AGAGAATATT
* * * *
265083 TGTCCCGAAGGACCATTACGTTCTGAAGGACCACTAGATATGTCCTGAAGGACCACTG
1 TGTCCCGAAGGACCACTACGTCCAGAAGGACCACTAGATATGTCCCGAAGGACCACTG
*
265141 TGTCCCGAAGGACCACTACGTCCAGAAGGACCACTGGATATGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTACGTCCAGAAGGACCACTAGATATGTCCCGAAGGACCACTG
265199 GAACCCTCGA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (58 bp):
TGTCCCGAAGGACCACTACGTCCAGAAGGACCACTAGATATGTCCCGAAGGACCACTG
Found at i:265200 original size:22 final size:21
Alignment explanation
Indices: 265083--265198 Score: 97
Period size: 18 Copynumber: 5.9 Consensus size: 21
265073 AGAGAATATT
265083 TGTCCCGAAGGACCA-T--TA
1 TGTCCCGAAGGACCACTGATA
* * *
265101 CGTTCTGAAGGACCACTAGATA
1 TGTCCCGAAGGACCACT-GATA
*
265123 TGTCCTGAAGGACCACTG---
1 TGTCCCGAAGGACCACTGATA
265141 TGTCCCGAAGGACCAC---TA
1 TGTCCCGAAGGACCACTGATA
* *
265159 CGTCCAGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACT-GATA
265181 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
265199 GAACCCTCGA
Statistics
Matches: 78, Mismatches: 10, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
18 41 0.53
19 1 0.01
21 2 0.03
22 34 0.44
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.19
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGATA
Found at i:268208 original size:24 final size:26
Alignment explanation
Indices: 268181--268233 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
268171 CCAAAGTTTG
268181 TAAGGCTGCAAACATCTT-TCTA-CT
1 TAAGGCTGCAAACATCTTCTCTATCT
**
268205 TAAGGCTGCACTCATCTTCTCTATCT
1 TAAGGCTGCAAACATCTTCTCTATCT
268231 TAA
1 TAA
268234 ATTCAACTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.64
25 4 0.16
26 5 0.20
ACGTcount: A:0.26, C:0.26, G:0.11, T:0.36
Consensus pattern (26 bp):
TAAGGCTGCAAACATCTTCTCTATCT
Found at i:271406 original size:2 final size:2
Alignment explanation
Indices: 271399--271443 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
271389 GTTTTAAAAC
271399 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
271441 AT A
1 AT A
271444 CCCCCATTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:271636 original size:24 final size:23
Alignment explanation
Indices: 271608--271673 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 23
271598 AGATATCAGA
* *
271608 AATCAAAATAGAATTCAGAACAT
1 AATCAGAATAGAATTCAGAACAG
*
271631 ATATCAGAATAGAATTCAGATCAG
1 A-ATCAGAATAGAATTCAGAACAG
271655 AATTCAGAATAGAATTCAG
1 AA-TCAGAATAGAATTCAG
271674 GGCATGTATC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 2 0.05
24 36 0.95
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (23 bp):
AATCAGAATAGAATTCAGAACAG
Found at i:271649 original size:12 final size:12
Alignment explanation
Indices: 271614--271673 Score: 70
Period size: 12 Copynumber: 5.0 Consensus size: 12
271604 CAGAAATCAA
271614 AATAGAATTCAG
1 AATAGAATTCAG
* *
271626 AACA-TATATCAG
1 AATAGAAT-TCAG
271638 AATAGAATTCAG
1 AATAGAATTCAG
271650 -ATCAGAATTCAG
1 AAT-AGAATTCAG
271662 AATAGAATTCAG
1 AATAGAATTCAG
271674 GGCATGTATC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
11 4 0.10
12 32 0.80
13 4 0.10
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.25
Consensus pattern (12 bp):
AATAGAATTCAG
Found at i:271710 original size:48 final size:48
Alignment explanation
Indices: 271602--271710 Score: 121
Period size: 48 Copynumber: 2.3 Consensus size: 48
271592 AAATGGAGAT
* * *
271602 ATCAGAAATCAAAATAGAATTCAGAACATATATCAGAATAGAATTCAG
1 ATCAGAAATCAGAATAGAATTCAGAACATATATCAGAACAGAATTCAA
* ** * * *
271650 ATCAGAATTCAGAATAGAATTCAGGGCATGTATCATAACAGTATTCAA
1 ATCAGAAATCAGAATAGAATTCAGAACATATATCAGAACAGAATTCAA
271698 ATC-GAAAATCAGA
1 ATCAG-AAATCAGA
271711 TAAAATATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.02
48 49 0.98
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.24
Consensus pattern (48 bp):
ATCAGAAATCAGAATAGAATTCAGAACATATATCAGAACAGAATTCAA
Found at i:274285 original size:13 final size:13
Alignment explanation
Indices: 274267--274294 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
274257 CTATATAGCG
274267 TTTAGACAGATCT
1 TTTAGACAGATCT
274280 TTTAGACAGATCT
1 TTTAGACAGATCT
274293 TT
1 TT
274295 ATAGCGTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (13 bp):
TTTAGACAGATCT
Found at i:274761 original size:24 final size:24
Alignment explanation
Indices: 274721--274825 Score: 81
Period size: 24 Copynumber: 4.4 Consensus size: 24
274711 TCGGAGATAT
* * *
274721 CAGAAATCAAAAAAGAATTTAGAA
1 CAGAAATCATAACAGAATTCAGAA
*
274745 CA-AATATCATAACAGAATTCAGAT
1 CAGAA-ATCATAACAGAATTCAGAA
* **
274769 CAGAAATTATAACAGAATTCAGGT
1 CAGAAATCATAACAGAATTCAGAA
* *
274793 CATG-TATCAGAACAGAATTCA-AA
1 CA-GAAATCATAACAGAATTCAGAA
274816 TCAGAAATCA
1 -CAGAAATCA
274826 GATAAAATAT
Statistics
Matches: 64, Mismatches: 12, Indels: 10
0.74 0.14 0.12
Matches are distributed among these distances:
23 3 0.05
24 58 0.91
25 3 0.05
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.22
Consensus pattern (24 bp):
CAGAAATCATAACAGAATTCAGAA
Found at i:274786 original size:48 final size:48
Alignment explanation
Indices: 274719--274825 Score: 124
Period size: 48 Copynumber: 2.2 Consensus size: 48
274709 AATCGGAGAT
* * *
274719 ATCAGAAATCAAAAAAGAATTTAGAACAAATATCATAACAGAATTCAG
1 ATCAGAAATCAAAAAAGAATTCAGAACAAATATCAGAACAGAATTCAA
* * * ** **
274767 ATCAGAAATTATAACAGAATTCAGGTCATGTATCAGAACAGAATTCAA
1 ATCAGAAATCAAAAAAGAATTCAGAACAAATATCAGAACAGAATTCAA
274815 ATCAGAAATCA
1 ATCAGAAATCA
274826 GATAAAATAT
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.22
Consensus pattern (48 bp):
ATCAGAAATCAAAAAAGAATTCAGAACAAATATCAGAACAGAATTCAA
Found at i:279378 original size:18 final size:18
Alignment explanation
Indices: 279355--279443 Score: 74
Period size: 18 Copynumber: 4.7 Consensus size: 18
279345 ATATTTGTCC
*
279355 CGAAGGACCATTACGTCT
1 CGAAGGACCACTACGTCT
*
279373 CGAAGGACCACTGGATATGT-T
1 CGAAGGACCAC----TACGTCT
*
279394 CCGAAGGACCACTATGTC-
1 -CGAAGGACCACTACGTCT
*
279412 CTGAAGGACCACTACGTCC
1 C-GAAGGACCACTACGTCT
279431 CGAAGGACCACTA
1 CGAAGGACCACTA
279444 GATATGTCCC
Statistics
Matches: 60, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
17 1 0.02
18 42 0.70
19 1 0.02
21 1 0.02
22 15 0.25
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (18 bp):
CGAAGGACCACTACGTCT
Found at i:279401 original size:22 final size:22
Alignment explanation
Indices: 279350--279487 Score: 129
Period size: 22 Copynumber: 6.8 Consensus size: 22
279340 AGAGAATATT
279350 TGTCCCGAAGGACCA-T---TA
1 TGTCCCGAAGGACCACTGGATA
* *
279368 CGTCTCGAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTGGATA
*
279390 TGTTCCGAAGGACCAC----TA
1 TGTCCCGAAGGACCACTGGATA
*
279408 TGTCCTGAAGGACCAC----TA
1 TGTCCCGAAGGACCACTGGATA
* *
279426 CGTCCCGAAGGACCACTAGATA
1 TGTCCCGAAGGACCACTGGATA
*
279448 TGTCCCAAAGGACCACTGGATA
1 TGTCCCGAAGGACCACTGGATA
279470 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTG
279488 TAACCCTCGA
Statistics
Matches: 99, Mismatches: 13, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
18 45 0.45
19 1 0.01
22 53 0.54
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTGGATA
Done.