Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002917.1 Hibiscus syriacus cultivar Beakdansim tig00006030_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: 263168
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:147213 original size:2 final size:2
Alignment explanation
Indices: 147206--147243 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
147196 TAAAACCTTA
147206 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
147244 TACTTGTTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:150809 original size:36 final size:36
Alignment explanation
Indices: 150760--150860 Score: 148
Period size: 36 Copynumber: 2.8 Consensus size: 36
150750 TAACATCAAC
* * *
150760 ACTTGAATAGAAAGTGCTGATGCCTCCTTCCCTTCG
1 ACTTGAATCGAAAGTGCAGATGCTTCCTTCCCTTCG
* *
150796 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCGTTCG
1 ACTTGAATCGAAAGTGCAGATGCTTCCTTCCCTTCG
*
150832 ACTTGAATCAAAAGTGCAGATGCTTCCTT
1 ACTTGAATCGAAAGTGCAGATGCTTCCTT
150861 TCGTTCTTCT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.31
Consensus pattern (36 bp):
ACTTGAATCGAAAGTGCAGATGCTTCCTTCCCTTCG
Found at i:152047 original size:20 final size:20
Alignment explanation
Indices: 152022--152071 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
152012 AGAAAATGGC
152022 TTACAATGATATTCAACACA
1 TTACAATGATATTCAACACA
152042 TTACAATGATATTCAACACA
1 TTACAATGATATTCAACACA
152062 TTACAATGAT
1 TTACAATGAT
152072 TGAGTATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (20 bp):
TTACAATGATATTCAACACA
Found at i:154005 original size:64 final size:64
Alignment explanation
Indices: 153937--154074 Score: 181
Period size: 64 Copynumber: 2.2 Consensus size: 64
153927 TTGAATGTGT
* **
153937 ATCGATGCATTAGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAACATCAAATGCAATTCGTG
1 ATCGATGCATAAGTAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCAAATGCAATTCGTG
154000 C
64 C
* * * *
154001 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAGTGAAACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
154065 ATCGATGCAT
1 ATCGATGCAT
154075 CCCAGCAATA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 62 0.95
65 3 0.05
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAATAAAACATCAAATGCAATTCGTGC
Found at i:154464 original size:12 final size:12
Alignment explanation
Indices: 154446--154481 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
154436 TATATATGTT
154446 CATGTGATATGA
1 CATGTGATATGA
*
154458 TATGTGATATGA
1 CATGTGATATGA
154470 CATGTGATATGA
1 CATGTGATATGA
154482 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:154490 original size:25 final size:24
Alignment explanation
Indices: 154462--154514 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
154452 ATATGATATG
*
154462 TGATATGACATGTGATATGAGA-ACA
1 TGATATGA-A-GTGATATAAGATACA
154487 TGATATGAAGTGATATAAGATACA
1 TGATATGAAGTGATATAAGATACA
154511 TGAT
1 TGAT
154515 CACAAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 8 0.31
25 8 0.31
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.30
Consensus pattern (24 bp):
TGATATGAAGTGATATAAGATACA
Found at i:154649 original size:15 final size:15
Alignment explanation
Indices: 154626--154659 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
154616 GAGGGTATAA
*
154626 TAGTTCTTCGGGATG
1 TAGTCCTTCGGGATG
154641 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
154656 TAGT
1 TAGT
154660 GGTCCTATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.32, T:0.38
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:160931 original size:64 final size:64
Alignment explanation
Indices: 160863--161019 Score: 181
Period size: 64 Copynumber: 2.5 Consensus size: 64
160853 TTAAATGTGT
* ** * * *
160863 ATCGATGCATTAGTAGTGCATCGATGCATCCCATTAATAGTGA-AACATCGAATGCAATTGGTGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAAT-ACAACATCGAATACAATTGATGC
* * ** *
160927 ATCGATGCATAAGGAGTGCATCGATGCATCCCAGCAATAATACTACATCGAATACCTTTTATGC
1 ATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACAACATCGAATACAATTGATGC
* *
160991 ACCGATGCATCAGTAGTGCATCGATGCAT
1 ATCGATGCATAAGTAGTGCATCGATGCAT
161020 ACCTTCATTA
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
63 1 0.01
64 77 0.99
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (64 bp):
ATCGATGCATAAGTAGTGCATCGATGCATCCCAGCAATAATACAACATCGAATACAATTGATGC
Found at i:161345 original size:12 final size:12
Alignment explanation
Indices: 161327--161362 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
161317 TATATATGTT
161327 CATGTGATATGA
1 CATGTGATATGA
*
161339 TATGTGATATGA
1 CATGTGATATGA
161351 CATGTGATATGA
1 CATGTGATATGA
161363 GAACATGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.36
Consensus pattern (12 bp):
CATGTGATATGA
Found at i:161371 original size:25 final size:24
Alignment explanation
Indices: 161343--161395 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
161333 ATATGATATG
*
161343 TGATATGACATGTGATATGAGA-ACA
1 TGATATGA-A-GTGATATAAGATACA
161368 TGATATGAAGTGATATAAGATACA
1 TGATATGAAGTGATATAAGATACA
161392 TGAT
1 TGAT
161396 CACAAGAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 10 0.38
24 8 0.31
25 8 0.31
ACGTcount: A:0.42, C:0.06, G:0.23, T:0.30
Consensus pattern (24 bp):
TGATATGAAGTGATATAAGATACA
Found at i:161525 original size:15 final size:15
Alignment explanation
Indices: 161507--161540 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
161497 GAGGGTATAA
*
161507 TAGTTCTTCGGGATG
1 TAGTCCTTCGGGATG
161522 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
161537 TAGT
1 TAGT
161541 GGTCCTACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.32, T:0.38
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:163562 original size:2 final size:2
Alignment explanation
Indices: 163557--163597 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
163547 ACACACACAC
163557 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
163598 ATTTTATTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:164670 original size:22 final size:22
Alignment explanation
Indices: 164645--164711 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
164635 AGAATAATGA
164645 TTGTTATATAACGATAAAGGTG
1 TTGTTATATAACGATAAAGGTG
* *
164667 TTGTCTA-A-AATCG-T-TA-TTG
1 TTGT-TATATAA-CGATAAAGGTG
*
164686 TTGTTATATAATGATAAAGGTG
1 TTGTTATATAACGATAAAGGTG
164708 TTGT
1 TTGT
164712 CTAAAATCGT
Statistics
Matches: 33, Mismatches: 5, Indels: 14
0.63 0.10 0.27
Matches are distributed among these distances:
18 2 0.06
19 8 0.24
20 4 0.12
21 4 0.12
22 13 0.39
23 2 0.06
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.43
Consensus pattern (22 bp):
TTGTTATATAACGATAAAGGTG
Found at i:164702 original size:41 final size:41
Alignment explanation
Indices: 164645--164725 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
164635 AGAATAATGA
164645 TTGTTATATAACGATAAAGGTGTTGTCTAAAATCGTTATTG
1 TTGTTATATAACGATAAAGGTGTTGTCTAAAATCGTTATTG
*
164686 TTGTTATATAATGATAAAGGTGTTGTCTAAAATCGTTATT
1 TTGTTATATAACGATAAAGGTGTTGTCTAAAATCGTTATT
164726 ACACAACTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (41 bp):
TTGTTATATAACGATAAAGGTGTTGTCTAAAATCGTTATTG
Found at i:167175 original size:14 final size:14
Alignment explanation
Indices: 167156--167185 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
167146 GATTGTAACA
167156 CTCTAAACCTAAGC
1 CTCTAAACCTAAGC
*
167170 CTCTAAACCTGAGC
1 CTCTAAACCTAAGC
167184 CT
1 CT
167186 AAAGTGTCAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.37, G:0.10, T:0.23
Consensus pattern (14 bp):
CTCTAAACCTAAGC
Found at i:167983 original size:17 final size:16
Alignment explanation
Indices: 167952--167991 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
167942 ATATCTTTTA
167952 AAATAA-TTTAAAGAT
1 AAATAATTTTAAAGAT
167967 AAATAATTTTAAAAGAT
1 AAATAATTTT-AAAGAT
*
167984 AAAAAATT
1 AAATAATT
167992 ATATGTGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 6 0.27
16 3 0.14
17 13 0.59
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
AAATAATTTTAAAGAT
Found at i:171059 original size:260 final size:258
Alignment explanation
Indices: 170465--171485 Score: 1352
Period size: 260 Copynumber: 3.9 Consensus size: 258
170455 ATATGAATCT
* *** * * * * *
170465 TACCCAAAGGTCTTATAGATGGTTCGAATAACTTATCATCTTACTCGAAAGACTGATAGATAACC
1 TACCCGAAGGTCTTATAGATGACCCGAATGACTTAACATCTTGCTCGAAAGACTGACAGATGACC
* * * * **
170530 CAAAGAATTTAATCATCATGCTCAAAAGACTTACTGATGGCCCGAAGAACTTAACAATTTTATAA
66 CAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
*
170595 ATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTT-AAAAATTTCATTTTTTGAA
131 ATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTAGAA
* * * * *
170659 AATATTAAATCATAAACTTTGAAAATCACTTTCTCATTTTTTGAAAATCATGTGAAAACATCC
196 AAGATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCC
* * * * * *
170722 TACCCGAAGGTCTTATGGAAGGCCCAAATGACTTATCATCTTGCTCGAAAGACTTACAGAT-AGC
1 TACCCGAAGGTCTTATAGATGACCCGAATGACTTAACATCTTGCTCGAAAGACTGACAGATGA-C
* * * *
170786 CCGAAGGATTTAATCATTATGCTCGAAAGATTTACTGATGGCCCGAAGGACTTACTAATTTTGGA
65 CCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGA
*
170851 AATAGTTTACT-GTGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTAATTTTTAG
130 AATAGTTTACTAG-GTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTAG
*
170915 AAAAGATTTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCAAAAATCATGTGAAAAACAT
194 AAAAGA-TTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTG-AAAACAT
170980 CC
257 CC
* *
170982 TACCTGAAGGTCTTATAGATGACCCGAATGACTTAACATCTTGCTCGAAAGACTGACAAATGACC
1 TACCCGAAGGTCTTATAGATGACCCGAATGACTTAACATCTTGCTCGAAAGACTGACAGATGACC
* * * * *
171047 CAAAGGATTTAATCATCATACTCGAAAAACTTACTGATGGCCTGAAGGACTTACCGACTTTGGAA
66 CAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
* * *
171112 AGAGTTTACTAGGTAAGAAACTTTTGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTTGAA
131 ATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTAGAA
* ** *
171177 AA-ATTTTAAATGAGAAAATTTGGAAATTGCTTTCTCATTTTTCGAAAATCATGTGGAAACATCC
196 AAGA--TTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCC
* * * * *
171241 TGCCCGAATGTCTTATAGATGACCCGAAGGACTTAACATCTTGCTCGATAGA-TAAACAGATGAC
1 TACCCGAAGGTCTTATAGATGACCCGAATGACTTAACATCTTGCTCGAAAGACT-GACAGATGAC
** * * *
171305 CTGAAGGATTTAATCATCATGCTTGAAACACTTACTGATAGCCCGAAGGACTTACCAATTTTGGA
65 CCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGA
* * *
171370 AATAGTTTA-TTGGTTAAGAAACTTTGGAAATCGTTTTCTTACTTTTCAAAAATTTCATTTTCAG
130 AATAGTTTACTAGG-TAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTAG
* * * *
171434 AAAAGATTAAATGAGAAACTTTGGAAATCATTTTTTAATTTTTTGAAAATCA
194 AAAAGATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCA
171486 CTTAATGATC
Statistics
Matches: 670, Mismatches: 83, Indels: 21
0.87 0.11 0.03
Matches are distributed among these distances:
256 2 0.00
257 151 0.23
258 63 0.09
259 223 0.33
260 229 0.34
261 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (258 bp):
TACCCGAAGGTCTTATAGATGACCCGAATGACTTAACATCTTGCTCGAAAGACTGACAGATGACC
CAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAA
ATAGTTTACTAGGTAAGAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCATTTTTAGAA
AAGATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTTCGAAAATCATGTGAAAACATCC
Found at i:173563 original size:9 final size:9
Alignment explanation
Indices: 173521--173602 Score: 51
Period size: 9 Copynumber: 8.3 Consensus size: 9
173511 ACTTGATTTG
*
173521 TTCTCTTTC
1 TTCTCTTTT
173530 TTCTTCTTCTT
1 TTC-TCTT-TT
173541 TT-TCTTATT
1 TTCTCTT-TT
173550 TTCTCTTTT
1 TTCTCTTTT
173559 TTCTCATCTTT
1 TTCTC-T-TTT
*
173570 TTGGCTTTTTT
1 TT--CTCTTTT
173581 ATTCT-TTTT
1 -TTCTCTTTT
173590 TGTCTCTTTT
1 T-TCTCTTTT
173600 TTC
1 TTC
173603 GAATTTGAAT
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
8 1 0.02
9 27 0.45
10 16 0.27
11 11 0.18
12 3 0.05
13 2 0.03
ACGTcount: A:0.04, C:0.21, G:0.04, T:0.72
Consensus pattern (9 bp):
TTCTCTTTT
Found at i:173580 original size:29 final size:27
Alignment explanation
Indices: 173521--173600 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 27
173511 ACTTGATTTG
*
173521 TTCTCTTTCTTCTTCTTCTTTTTCTTATT
1 TTCTCTTTTTTC-TC-TCTTTTTCTTATT
173550 TTCTCTTTTTTCTCATCTTTTTGGCTT-TT
1 TTCTCTTTTTTCTC-TCTTTTT--CTTATT
* *
173579 TTATTCTTTTTTGTCTCTTTTT
1 TT-CTCTTTTTTCTCTCTTTTT
173601 TCGAATTTGA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
28 9 0.20
29 22 0.50
30 13 0.30
ACGTcount: A:0.04, C:0.20, G:0.04, T:0.72
Consensus pattern (27 bp):
TTCTCTTTTTTCTCTCTTTTTCTTATT
Found at i:175592 original size:63 final size:63
Alignment explanation
Indices: 175458--175597 Score: 158
Period size: 62 Copynumber: 2.2 Consensus size: 63
175448 ATTGTTCAGT
* *
175458 GTGTATCGATGCACCCATTAAAAATGGAAACATCGAATGCAATTAGTGCATCGATGCATAAGG
1 GTGTATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTAGTGCATCGATGCATAAGG
* * * ** * * *
175521 GTGCATCGATGCACCCCTT-AAAATGAAAATATCGAAGGTGATTGGTGTATCGATGCAT-GGG
1 GTGTATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTAGTGCATCGATGCATAAGG
175582 TAGTGTATCGATGCAC
1 --GTGTATCGATGCAC
175598 TTCAAGGGAA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
61 2 0.03
62 32 0.50
63 30 0.47
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (63 bp):
GTGTATCGATGCACCCATTAAAAATGAAAACATCGAAGGCAATTAGTGCATCGATGCATAAGG
Found at i:176744 original size:2 final size:2
Alignment explanation
Indices: 176737--176809 Score: 130
Period size: 2 Copynumber: 37.0 Consensus size: 2
176727 GAACATGTGA
*
176737 AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
176778 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
176810 GATAAGACTA
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.01
2 67 0.99
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:177230 original size:23 final size:23
Alignment explanation
Indices: 177197--177264 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
177187 AACCTTATAT
177197 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * * *
177220 GGCACTACGGTGTAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
177243 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
177265 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:184026 original size:20 final size:19
Alignment explanation
Indices: 183983--184026 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
183973 TGAGAGGTAT
*
183983 TAAAATAGTAACATAAACC
1 TAAAATAGTAACATAAAAC
* *
184002 TAAAATATTAGCATAAAAAC
1 TAAAATAGTAACAT-AAAAC
184022 TAAAA
1 TAAAA
184027 AAAAAATCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.61, C:0.11, G:0.05, T:0.23
Consensus pattern (19 bp):
TAAAATAGTAACATAAAAC
Found at i:188380 original size:17 final size:17
Alignment explanation
Indices: 188358--188406 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
188348 AATTGAAAAA
188358 ATATAATATATATATAC
1 ATATAATATATATATAC
* *
188375 ATATAATATA-AGTTTAT
1 ATATAATATATA-TATAC
188392 ATATAAGTATATATA
1 ATATAA-TATATATA
188407 AAATGTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 1 0.04
17 19 0.73
18 5 0.19
19 1 0.04
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (17 bp):
ATATAATATATATATAC
Found at i:188395 original size:12 final size:12
Alignment explanation
Indices: 188358--188406 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
188348 AATTGAAAAA
188358 ATATAA-TATAT
1 ATATAAGTATAT
188369 ATATACA-TATA-
1 ATATA-AGTATAT
*
188380 ATATAAGTTTAT
1 ATATAAGTATAT
188392 ATATAAGTATAT
1 ATATAAGTATAT
188404 ATA
1 ATA
188407 AAATGTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
10 1 0.03
11 13 0.39
12 19 0.58
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (12 bp):
ATATAAGTATAT
Found at i:188469 original size:2 final size:2
Alignment explanation
Indices: 188456--188490 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
188446 ATTTATATTA
188456 AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
188491 TATTATAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:188497 original size:8 final size:9
Alignment explanation
Indices: 188449--188497 Score: 57
Period size: 10 Copynumber: 5.4 Consensus size: 9
188439 AACTATAATT
188449 TATATTA-A
1 TATATTATA
*
188457 TATAGTATA
1 TATATTATA
188466 TATATATATA
1 TATAT-TATA
188476 TATATATATA
1 TATAT-TATA
188486 TATATTAT-
1 TATATTATA
188494 TATA
1 TATA
188498 AGTAAGTAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
8 10 0.27
9 8 0.22
10 19 0.51
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (9 bp):
TATATTATA
Found at i:188586 original size:20 final size:20
Alignment explanation
Indices: 188561--188618 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 20
188551 TTTATTTGGG
188561 AATTTAGAGGGAAATTGAGA
1 AATTTAGAGGGAAATTGAGA
*
188581 AATTTAGAGGG-AATAGA-A
1 AATTTAGAGGGAAATTGAGA
* *
188599 AATTTGGAGAGAAATTGAGA
1 AATTTAGAGGGAAATTGAGA
188619 TTGAGATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 10 0.31
19 10 0.31
20 12 0.38
ACGTcount: A:0.47, C:0.00, G:0.29, T:0.24
Consensus pattern (20 bp):
AATTTAGAGGGAAATTGAGA
Found at i:189048 original size:13 final size:13
Alignment explanation
Indices: 189025--189080 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
189015 ATAAATCATG
*
189025 TATAGTATATAAAC
1 TATA-TATATAAAT
*
189039 TATATATATATAT
1 TATATATATAAAT
*
189052 TATATTTATAAAT
1 TATATATATAAAT
*
189065 TATATAAAATAAAT
1 TATAT-ATATAAAT
189079 TA
1 TA
189081 CTTATATAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
13 23 0.66
14 12 0.34
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (13 bp):
TATATATATAAAT
Found at i:189580 original size:12 final size:13
Alignment explanation
Indices: 189560--189613 Score: 58
Period size: 12 Copynumber: 4.2 Consensus size: 13
189550 ACCAGTATAG
189560 TATATATAAACTA
1 TATATATAAACTA
*
189573 TA-ATATAACCTCTA
1 TATATATAA--ACTA
*
189587 TATATATATA-TA
1 TATATATAAACTA
189599 TATATATAAACTA
1 TATATATAAACTA
189612 TA
1 TA
189614 AACTAAATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
12 17 0.52
13 6 0.18
14 5 0.15
15 5 0.15
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:189728 original size:29 final size:28
Alignment explanation
Indices: 189684--189752 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 28
189674 TAGTTTATAA
*
189684 AAACTCTAAACCTTAAATCATAAACCTT
1 AAACCCTAAACCTTAAATCATAAACCTT
* *
189712 AAACCCCTAAACTTTAAGTCATAAACCTT
1 AAA-CCCTAAACCTTAAATCATAAACCTT
189741 AAACCCTAAACC
1 AAACCCTAAACC
189753 ATAATATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
28 11 0.31
29 25 0.69
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (28 bp):
AAACCCTAAACCTTAAATCATAAACCTT
Found at i:189750 original size:14 final size:14
Alignment explanation
Indices: 189684--189752 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
189674 TAGTTTATAA
*
189684 AAACTCTAAACCTT
1 AAACCCTAAACCTT
* *
189698 AAATCATAAACCTT
1 AAACCCTAAACCTT
*
189712 AAACCCCTAAACTTT
1 AAA-CCCTAAACCTT
** *
189727 AAGTCATAAACCTT
1 AAACCCTAAACCTT
189741 AAACCCTAAACC
1 AAACCCTAAACC
189753 ATAATATAAA
Statistics
Matches: 41, Mismatches: 13, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
14 31 0.76
15 10 0.24
ACGTcount: A:0.45, C:0.29, G:0.01, T:0.25
Consensus pattern (14 bp):
AAACCCTAAACCTT
Found at i:189861 original size:20 final size:20
Alignment explanation
Indices: 189836--189884 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
189826 AAAGTAATGT
189836 AAATGGACTAGCACTATTAC
1 AAATGGACTAGCACTATTAC
* * *
189856 AAATGGACTAGTATTATTGC
1 AAATGGACTAGCACTATTAC
189876 AAATGGACT
1 AAATGGACT
189885 TATTTTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (20 bp):
AAATGGACTAGCACTATTAC
Found at i:191850 original size:13 final size:13
Alignment explanation
Indices: 191818--191844 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
191808 TAATTTACAT
191818 TTAAATAATTTTA
1 TTAAATAATTTTA
191831 TTAAATAATTTTA
1 TTAAATAATTTTA
191844 T
1 T
191845 ATAATATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:191895 original size:17 final size:18
Alignment explanation
Indices: 191868--191906 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
191858 ATAAACCATG
*
191868 TATAGTATATATAACCTA
1 TATAGTATATATAAACTA
191886 TATA-TATATATAAACTA
1 TATAGTATATATAAACTA
191903 TATA
1 TATA
191907 AAGTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (18 bp):
TATAGTATATATAAACTA
Found at i:191998 original size:49 final size:49
Alignment explanation
Indices: 191895--191988 Score: 154
Period size: 48 Copynumber: 1.9 Consensus size: 49
191885 ATATATATAT
* **
191895 ATAAACTATATAAAGTATATTACTTATATAGTTTATAGAAACACTATCC
1 ATAAACTATATAAAGTATATAAAGTATATAGTTTATAGAAACACTATCC
191944 ATAAACTATATAAAGTA-ATAAAGTATATAGTTTATAGAAACACTA
1 ATAAACTATATAAAGTATATAAAGTATATAGTTTATAGAAACACTA
191989 AATCATAAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
48 25 0.60
49 17 0.40
ACGTcount: A:0.49, C:0.10, G:0.07, T:0.34
Consensus pattern (49 bp):
ATAAACTATATAAAGTATATAAAGTATATAGTTTATAGAAACACTATCC
Found at i:192438 original size:2 final size:2
Alignment explanation
Indices: 192382--192429 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
192372 ATAAACCATG
192382 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
192424 TA TA TA
1 TA TA TA
192430 AACTATATAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:195143 original size:20 final size:20
Alignment explanation
Indices: 195118--195225 Score: 157
Period size: 20 Copynumber: 5.4 Consensus size: 20
195108 TTTTCCTAAT
* *
195118 TCGCAAGGCGGATACGTAAA
1 TCGCAACGCGAATACGTAAA
195138 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
195158 TCGCAACGCGAATACGTAAA
1 TCGCAACGCGAATACGTAAA
195178 TCGCAACGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
*
195198 TCGCAATGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
195218 TCGCAACG
1 TCGCAACG
195226 AGATTCTGAC
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
19 1 0.01
20 82 0.99
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:196112 original size:24 final size:24
Alignment explanation
Indices: 196085--196138 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
196075 GTATTCAAAA
196085 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
196109 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
196133 TTTGAT
1 TTTGAT
196139 GATTTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:198587 original size:20 final size:20
Alignment explanation
Indices: 198562--198650 Score: 117
Period size: 20 Copynumber: 4.5 Consensus size: 20
198552 TAACGCGAAA
*
198562 ATCGCAATGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
198582 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* *
198602 ATCGCAATGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
*
198622 ATCGCAACGCAGAAATGACT
1 ATCGCAACGCGGAAATGACT
198642 ATCGCAACG
1 ATCGCAACG
198651 AGAGAATCGC
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
20 57 0.95
21 3 0.05
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:198621 original size:40 final size:40
Alignment explanation
Indices: 198562--198648 Score: 140
Period size: 40 Copynumber: 2.2 Consensus size: 40
198552 TAACGCGAAA
*
198562 ATCGCAATGCGAATATGACTATCGCAACACGGAAATGACT
1 ATCGCAATGCGAATATGACTATCGCAACACAGAAATGACT
*
198602 ATCGCAATGCGGAAT-TGACTATCGCAACGCAGAAATGACT
1 ATCGCAATGC-GAATATGACTATCGCAACACAGAAATGACT
198642 ATCGCAA
1 ATCGCAA
198649 CGAGAGAATC
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 40 0.91
41 4 0.09
ACGTcount: A:0.37, C:0.23, G:0.21, T:0.20
Consensus pattern (40 bp):
ATCGCAATGCGAATATGACTATCGCAACACAGAAATGACT
Found at i:198672 original size:33 final size:33
Alignment explanation
Indices: 198622--198714 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
198612 GGAATTGACT
* **
198622 ATCGCAACGCAGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
198656 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
198689 ATCGCAATGCGAAAATGAAAACCGCA
1 ATCGCAATGCG-AAATGAAAATCGCA
198715 TTACGATTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
33 31 0.58
34 22 0.42
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:198748 original size:33 final size:33
Alignment explanation
Indices: 198711--198777 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
198701 AAATGAAAAC
**
198711 CGCATTACGATTCACTCGTTGCGATTTTCATTT
1 CGCATTACGATTCACTCGTTGCGATAGTCATTT
* *
198744 CGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 CGCATTACGATTCACTCGTTGCGATAGTCATTT
198777 C
1 C
198778 CGCGTTGCGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.40
Consensus pattern (33 bp):
CGCATTACGATTCACTCGTTGCGATAGTCATTT
Found at i:200311 original size:21 final size:21
Alignment explanation
Indices: 200282--200368 Score: 75
Period size: 21 Copynumber: 4.1 Consensus size: 21
200272 GAATGTTGGG
*
200282 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTCAACGATGAC
* * * **
200303 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTCAACGATGAC
* * ** *
200324 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTCAACGATGAC
200345 AGGGGCCTCTTCAACGATGAC
1 AGGGGCCTCTTCAACGATGAC
200366 AGG
1 AGG
200369 TGAGTCGGGC
Statistics
Matches: 48, Mismatches: 18, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.23, C:0.21, G:0.36, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTCAACGATGAC
Found at i:200915 original size:20 final size:20
Alignment explanation
Indices: 200849--200897 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
200839 GAAACTTAAA
*
200849 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
200869 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
200889 ATCGCAATG
1 ATCGCAATG
200898 TTAATTTGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:200965 original size:20 final size:20
Alignment explanation
Indices: 200940--201039 Score: 140
Period size: 20 Copynumber: 5.3 Consensus size: 20
200930 TGCGAAATGA
200940 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
200960 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
*
200980 GAT--TC--TCTCG--TTGC
1 GATAGTCATTTTCGCATTGC
*
200994 GATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
201014 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
201034 GATAGT
1 GATAGT
201040 AAACTATTCT
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
14 7 0.10
16 6 0.08
18 6 0.08
20 52 0.73
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.40
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:202941 original size:20 final size:20
Alignment explanation
Indices: 202918--202957 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
202908 CTGAAACTTT
202918 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
202938 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
202958 CTATCACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.10
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:202967 original size:20 final size:20
Alignment explanation
Indices: 202918--202967 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
202908 CTGAAACTTT
*
202918 AAATCGCAACACGAAAATGA
1 AAATCACAACACGAAAATGA
*
202938 AAATCGCAACACGAAAATGA
1 AAATCACAACACGAAAATGA
**
202958 CTATCACAAC
1 AAATCACAAC
202968 GCAAGAATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (20 bp):
AAATCACAACACGAAAATGA
Found at i:203417 original size:22 final size:22
Alignment explanation
Indices: 203358--203417 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 22
203348 ATCGTGAATA
* *
203358 ATTTCGCCGGAGATGGAGACTG
1 ATTTCGTCGGAGATGGGGACTG
203380 -TTATCGTC---G-TGGGGACTG
1 ATT-TCGTCGGAGATGGGGACTG
203398 ATTTCGTCGGAGATGGGGAC
1 ATTTCGTCGGAGATGGGGAC
203418 GGATGTCGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 12
0.68 0.05 0.27
Matches are distributed among these distances:
18 13 0.43
19 3 0.10
21 3 0.10
22 11 0.37
ACGTcount: A:0.18, C:0.17, G:0.38, T:0.27
Consensus pattern (22 bp):
ATTTCGTCGGAGATGGGGACTG
Found at i:203619 original size:20 final size:20
Alignment explanation
Indices: 203594--203645 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
203584 GCTATGTAAA
203594 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
203614 TCGCATTGCGATAGTCAGAT
1 TCGCATTGCGATAGTCAGAT
203634 TCGCATTGCGAT
1 TCGCATTGCGAT
203646 TTACGTATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (20 bp):
TCGCATTGCGATAGTCAGAT
Found at i:203655 original size:20 final size:20
Alignment explanation
Indices: 203632--203684 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
203622 CGATAGTCAG
203632 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
203652 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
203672 ATTCGCATTGCGA
1 ATTCGCATTGCGA
203685 ATTAGGAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:210374 original size:27 final size:27
Alignment explanation
Indices: 210322--210384 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
210312 ACCGAAATTT
* * *
210322 TTTAAAATTTTCTAATTTATATAAAA-
1 TTTAAAATTTTCTAATTCAAAAAAAAG
*
210348 TTTAAATATTTTTTAATTCAAAAAAAAG
1 TTTAAA-ATTTTCTAATTCAAAAAAAAG
*
210376 TTTATAATT
1 TTTAAAATT
210385 AATTTAAATA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
26 6 0.20
27 19 0.63
28 5 0.17
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (27 bp):
TTTAAAATTTTCTAATTCAAAAAAAAG
Found at i:210667 original size:186 final size:188
Alignment explanation
Indices: 210339--210732 Score: 613
Period size: 186 Copynumber: 2.1 Consensus size: 188
210329 TTTTCTAATT
*
210339 TATATAA-A-ATTTAAATATTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATA
1 TATATAATATATTT-AATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATA
* * *
210402 TAATTATAAAATAAAAAATGTTATATAATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAG
65 TAATTATAAAATAAAAAATGTTATATAATTTGTTTAATTAATTAACATTGATTTAGATTTAAAAG
*
210467 TTATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAG-CCTATATGTTA
130 TTATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTAAGACC-ATATGTTA
210526 TATATAATATATTTAATATTTTTTAATTCAAAAAAAATAGTTTACAATTAATTTAAAT-A-ATAT
1 TATATAATATATTTAATATTTTTTAATTC-AAAAAAA-AGTTTACAATTAATTTAAATAATATAT
*
210589 ATAATTATAAAAT-AAAAATTTTATATAA-TTGTTTAATTAATTAACATTGATTTAGATTTAAAA
64 ATAATTATAAAATAAAAAATGTTATATAATTTGTTTAATTAATTAACATTGATTTAGATTTAAAA
* * *
210652 GTTATTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTAAGACCATATTTTA
129 GTTATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTAAGACCATATGTTA
*
210712 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
210733 AATTTCGGTT
Statistics
Matches: 192, Mismatches: 10, Indels: 11
0.90 0.05 0.05
Matches are distributed among these distances:
186 105 0.55
187 23 0.12
188 33 0.17
189 12 0.06
190 19 0.10
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (188 bp):
TATATAATATATTTAATATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAT
AATTATAAAATAAAAAATGTTATATAATTTGTTTAATTAATTAACATTGATTTAGATTTAAAAGT
TATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTAAGACCATATGTTA
Found at i:213225 original size:49 final size:49
Alignment explanation
Indices: 213172--213275 Score: 192
Period size: 49 Copynumber: 2.1 Consensus size: 49
213162 GTTTTAGATA
213172 AAATATTAATTTGATCTTAAATTTTATAAAAAATACTAATTTAACTCCT
1 AAATATTAATTTGATCTTAAATTTTATAAAAAATACTAATTTAACTCCT
*
213221 AAATATTAATTTGATCTTAAATTTTATATAAAATACTAATTTAACTCCT
1 AAATATTAATTTGATCTTAAATTTTATAAAAAATACTAATTTAACTCCT
213270 -AATATT
1 AAATATT
213276 TATGTAAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 6 0.11
49 48 0.89
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (49 bp):
AAATATTAATTTGATCTTAAATTTTATAAAAAATACTAATTTAACTCCT
Found at i:213255 original size:30 final size:31
Alignment explanation
Indices: 213221--213296 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
213211 TTTAACTCCT
* *
213221 AAATATTAATTTGA-TCTTAA-ATTTTATATA
1 AAATATTAATTTAACTCCTAATA-TTTATATA
* *
213251 AAATACTAATTTAACTCCTAATATTTATGTA
1 AAATATTAATTTAACTCCTAATATTTATATA
*
213282 AAATATCAATTTAAC
1 AAATATTAATTTAAC
213297 CCATGAGAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 12 0.32
31 25 0.66
32 1 0.03
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (31 bp):
AAATATTAATTTAACTCCTAATATTTATATA
Found at i:213293 original size:49 final size:49
Alignment explanation
Indices: 213188--213285 Score: 135
Period size: 49 Copynumber: 2.0 Consensus size: 49
213178 TAATTTGATC
* * **
213188 TTAAATTTTATAAAAAATACTAATTTAACTCCTAAATATTAATTTGATC
1 TTAAATTTTATAAAAAATACTAATTTAACTCCTAAATATTAATGTAAAA
* *
213237 TTAAATTTTATATAAAATACTAATTTAACTCCT-AATATTTATGTAAAA
1 TTAAATTTTATAAAAAATACTAATTTAACTCCTAAATATTAATGTAAAA
213285 T
1 T
213286 ATCAATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
48 11 0.26
49 32 0.74
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (49 bp):
TTAAATTTTATAAAAAATACTAATTTAACTCCTAAATATTAATGTAAAA
Found at i:214409 original size:16 final size:17
Alignment explanation
Indices: 214378--214421 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
214368 TCCTTTTTAT
214378 TATTATTTTATTATTTG
1 TATTATTTTATTATTTG
*
214395 TATTGTTTT-TTATTTG
1 TATTATTTTATTATTTG
*
214411 T-TCATTTTATT
1 TATTATTTTATT
214422 TTTTTATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 10 0.43
17 8 0.35
ACGTcount: A:0.18, C:0.02, G:0.07, T:0.73
Consensus pattern (17 bp):
TATTATTTTATTATTTG
Found at i:214441 original size:21 final size:21
Alignment explanation
Indices: 214400--214452 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
214390 ATTTGTATTG
**
214400 TTTTTTATTTGTTCATTTTAT
1 TTTTTTATTTCCTCATTTTAT
214421 TTTTTTATTTCCT-ATTATTAT
1 TTTTTTATTTCCTCATT-TTAT
*
214442 TATTATTATTT
1 T-TTTTTATTT
214453 TGTCTATACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 3 0.11
21 16 0.59
22 8 0.30
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTTTTATTTCCTCATTTTAT
Found at i:214486 original size:28 final size:28
Alignment explanation
Indices: 214434--214487 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
214424 TTTATTTCCT
*
214434 ATTATTATTATTATTATTTTGTCTATAC
1 ATTATTATTATTATTATATTGTCTATAC
214462 ATTATTA-TATATATATATATT-TCTAT
1 ATTATTATTAT-TAT-TATATTGTCTAT
214488 TTTTGTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 3 0.13
28 15 0.65
29 5 0.22
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (28 bp):
ATTATTATTATTATTATATTGTCTATAC
Found at i:214531 original size:17 final size:16
Alignment explanation
Indices: 214487--214537 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
214477 TATATTTCTA
*
214487 TTTTTGTTTATCCTTTTA
1 TTTTTGTTTAT--TTTTT
*
214505 TTTTT-ATTATTATTTT
1 TTTTTGTTTATT-TTTT
214521 TTTTTGTTTATTTTTT
1 TTTTTGTTTATTTTTT
214537 T
1 T
214538 GTTTATTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 1 0.04
16 13 0.46
17 9 0.32
18 5 0.18
ACGTcount: A:0.12, C:0.04, G:0.04, T:0.80
Consensus pattern (16 bp):
TTTTTGTTTATTTTTT
Found at i:214534 original size:12 final size:12
Alignment explanation
Indices: 214519--214546 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
214509 TATTATTATT
214519 TTTTTTTGTTTA
1 TTTTTTTGTTTA
214531 TTTTTTTGTTTA
1 TTTTTTTGTTTA
214543 TTTT
1 TTTT
214547 ATATCTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (12 bp):
TTTTTTTGTTTA
Found at i:216298 original size:64 final size:64
Alignment explanation
Indices: 216156--216318 Score: 248
Period size: 58 Copynumber: 2.6 Consensus size: 64
216146 CAAGACTTTT
216156 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCATTC
*
216220 AGAG------TCAACTTCACAGCGAAGGATATTGGACTCAACAAACAATTTTTCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCATTC
** *
216278 AGAGTCAATTTCAACTTCACATTGAAGGATATTGAACTCAA
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAA
216319 AGCAATACAA
Statistics
Matches: 89, Mismatches: 4, Indels: 12
0.85 0.04 0.11
Matches are distributed among these distances:
58 57 0.64
64 32 0.36
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAACAACTTTTCAGTTTCATTC
Found at i:216374 original size:55 final size:54
Alignment explanation
Indices: 216285--216479 Score: 179
Period size: 55 Copynumber: 3.7 Consensus size: 54
216275 TTCAGAGTCA
** ** *
216285 ATTTCAACTTCACATTGAAGGATATTGAACTCAAAGCAATACAACCAAATATTGG
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCAATACAA-CAAATATTGG
* * * * *
216340 ATTTCAACTTCACAACGAAGTATATCCAATTCAAATC-ATTC-A-GAGTCA----
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCAATACAACAAAT-ATTGG
** **
216388 ATTTCAACTTCACAGGGAAGGATATTGAATTCAAAGCAATACAATCAAATATTGG
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCAATACAA-CAAATATTGG
*
216443 ATTTCAACTTCACAACGAAAGATATCCAATTCAAAGC
1 ATTTCAACTTCACAACGAAGGATATCCAATTCAAAGC
216480 TCAACTTCAA
Statistics
Matches: 107, Mismatches: 24, Indels: 18
0.72 0.16 0.12
Matches are distributed among these distances:
48 31 0.29
49 3 0.03
50 1 0.01
51 3 0.03
52 3 0.03
53 1 0.01
54 3 0.03
55 62 0.58
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.27
Consensus pattern (54 bp):
ATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCAATACAACAAATATTGG
Found at i:216451 original size:103 final size:103
Alignment explanation
Indices: 216272--216477 Score: 360
Period size: 103 Copynumber: 2.0 Consensus size: 103
216262 TTTTTCAGTT
**
216272 TCATTCAGAGTCAATTTCAACTTCACATTGAAGGATATTGAACTCAAAGCAATACAACCAAATAT
1 TCATTCAGAGTCAATTTCAACTTCACAGGGAAGGATATTGAACTCAAAGCAATACAACCAAATAT
216337 TGGATTTCAACTTCACAACG-AAGTATATCCAATTCAAA
66 TGGATTTCAACTTCACAACGAAAG-ATATCCAATTCAAA
* *
216375 TCATTCAGAGTCAATTTCAACTTCACAGGGAAGGATATTGAATTCAAAGCAATACAATCAAATAT
1 TCATTCAGAGTCAATTTCAACTTCACAGGGAAGGATATTGAACTCAAAGCAATACAACCAAATAT
216440 TGGATTTCAACTTCACAACGAAAGATATCCAATTCAAA
66 TGGATTTCAACTTCACAACGAAAGATATCCAATTCAAA
216478 GCTCAACTTC
Statistics
Matches: 98, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 95 0.97
104 3 0.03
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (103 bp):
TCATTCAGAGTCAATTTCAACTTCACAGGGAAGGATATTGAACTCAAAGCAATACAACCAAATAT
TGGATTTCAACTTCACAACGAAAGATATCCAATTCAAA
Found at i:216612 original size:42 final size:42
Alignment explanation
Indices: 216505--216619 Score: 135
Period size: 43 Copynumber: 2.7 Consensus size: 42
216495 AGGAGCCATC
*
216505 CACGATTTCAACTCCACGACGAAGGATATCGTGCCCACACAT
1 CACGATTTCAACTTCACGACGAAGGATATCGTGCCCACACAT
* *
216547 CCACGATTTTAACTTCACGACGAAGGATATCGTG-TCAGCAACAT
1 -CACGATTTCAACTTCACGACGAAGGATATCGTGCCCA-C-ACAT
** *
216591 -TGGATTTCAACTTCACAACGAAGGATATC
1 CACGATTTCAACTTCACGACGAAGGATATC
216620 CAATTCAAAG
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
42 27 0.43
43 32 0.51
44 4 0.06
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (42 bp):
CACGATTTCAACTTCACGACGAAGGATATCGTGCCCACACAT
Found at i:217048 original size:137 final size:137
Alignment explanation
Indices: 216890--217568 Score: 1004
Period size: 137 Copynumber: 5.0 Consensus size: 137
216880 CCAATTCGAG
* * * *
216890 AACTCTTCATCACGAATGAGCAGCATCATCCTTAGATAGCCAGATGTCTTCATCACGAAGGAACC
1 AACTCCTCATCACGAAGGAGCAACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACC
* *
216955 GTGTTATCTCAAATATCTTCAAAGATTGTCAGAAC-TCCTCATCACGAAGGAACAATATCATCCA
66 GTGTTATCTCAAATATCTTCAAAGATGGTCAG-ACGTCCTCATCACGAAGGAACAATGTCATCCA
*
217019 CCTATCAA
130 CCGATCAA
*
217027 AACTCCTCATCACGAAGGAGCAACATCATCCTTAGATAGCCAGATGTTCTCATCACGAAGGAACC
1 AACTCCTCATCACGAAGGAGCAACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACC
* * *
217092 ATGTTATCTCAAATATCTTCAAAGATGGTCGGACTTCCTCATCACGAAGGAACAATGTCATCCAC
66 GTGTTATCTCAAATATCTTCAAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
217157 CGATCAA
131 CGATCAA
* * * *
217164 AACTCCTCATCACGAAAGAGCAACATCATCTTTAGATAGCTAGATGTCCTCATCACGAAGGAACT
1 AACTCCTCATCACGAAGGAGCAACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACC
* *
217229 GTGTTATCTCAAATATCATCAAAGATGGTCAGACGTCCTCATCACGAATGG-ACAATGTCATCTA
66 GTGTTATCTCAAATATCTTCAAAGATGGTCAGACGTCCTCATCACGAA-GGAACAATGTCATCCA
*
217293 CAGATCAA
130 CCGATCAA
* * *
217301 AACTCCTCATCACGAATGAGCAACATCATCCTTAGATAGCCAGATGTACTCATCACGAAGGAACT
1 AACTCCTCATCACGAAGGAGCAACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACC
* * * * *
217366 GTGTTATCTCAAATATCTTTAAATATGGTCAGACGTCCTTATCATGAAGGAATAATGTCATCCAC
66 GTGTTATCTCAAATATCTTCAAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
*
217431 CGATCAG
131 CGATCAA
* * *
217438 AACTCCTCATCACAAAGGAGCAACATCACCCTTAAATAGCCAGATGTCCTCATCACGAAGGAACC
1 AACTCCTCATCACGAAGGAGCAACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACC
* * * *
217503 GTGTTTTCTCAAATATCTTCAAAGATGGACAGACGTCCTTATCAC-AAGGAAACAATGTCATACA
66 GTGTTATCTCAAATATCTTCAAAGATGGTCAGACGTCCTCATCACGAAGG-AACAATGTCATCCA
217567 CC
130 CC
217569 AGTTGGATCT
Statistics
Matches: 491, Mismatches: 47, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
136 8 0.02
137 481 0.98
138 2 0.00
ACGTcount: A:0.34, C:0.26, G:0.15, T:0.25
Consensus pattern (137 bp):
AACTCCTCATCACGAAGGAGCAACATCATCCTTAGATAGCCAGATGTCCTCATCACGAAGGAACC
GTGTTATCTCAAATATCTTCAAAGATGGTCAGACGTCCTCATCACGAAGGAACAATGTCATCCAC
CGATCAA
Found at i:220667 original size:59 final size:59
Alignment explanation
Indices: 220602--220716 Score: 203
Period size: 59 Copynumber: 1.9 Consensus size: 59
220592 ATAAAGTCAA
* *
220602 ATTAATATTTTCGTATAATTGAATAAATATTATACCATTTTCTCGTTTTCTTTTTTAAT
1 ATTAATATTTTCGTATAATTGAATAAATATTATAACATTTTCTCATTTTCTTTTTTAAT
*
220661 ATTAATATTTTCGTATAATTGAATAAATGTTATAACATTTTCTCATTTTCTTTTTT
1 ATTAATATTTTCGTATAATTGAATAAATATTATAACATTTTCTCATTTTCTTTTTT
220717 TAAGTGTGTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 53 1.00
ACGTcount: A:0.30, C:0.10, G:0.05, T:0.55
Consensus pattern (59 bp):
ATTAATATTTTCGTATAATTGAATAAATATTATAACATTTTCTCATTTTCTTTTTTAAT
Found at i:222195 original size:21 final size:21
Alignment explanation
Indices: 222162--222208 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
222152 AAAAATAAAT
* *
222162 TTTATTGTTTTAATATATATTAA
1 TTTATT-TTTAAAAATAT-TTAA
222185 TTTATTTTTAAAAATATTTAA
1 TTTATTTTTAAAAATATTTAA
222206 TTT
1 TTT
222209 CAATTTTGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 9 0.41
23 6 0.27
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTATTTTTAAAAATATTTAA
Found at i:223285 original size:3 final size:3
Alignment explanation
Indices: 223277--223309 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
223267 GAATTGGGTT
223277 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
223310 CTTCGTGACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:224054 original size:2 final size:2
Alignment explanation
Indices: 224047--224101 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
224037 ATGCAAATGA
224047 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
224089 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
224102 GCTTAGGGAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:228793 original size:22 final size:22
Alignment explanation
Indices: 228766--228838 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
228756 TCACTCTCTA
*
228766 CGGCGACATCCGTACCCATCTC
1 CGGCGACATCCGTCCCCATCTC
* *
228788 TGGCGACATCCGTCCCCCTCTC
1 CGGCGACATCCGTCCCCATCTC
* *
228810 CGGCGACATTCGTCCCCATATC
1 CGGCGACATCCGTCCCCATCTC
*
228832 CGACGAC
1 CGGCGAC
228839 CCCCTCCATC
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.16, C:0.45, G:0.19, T:0.19
Consensus pattern (22 bp):
CGGCGACATCCGTCCCCATCTC
Found at i:229266 original size:20 final size:19
Alignment explanation
Indices: 229232--229269 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
229222 CGCATTGCGA
229232 ATTTTGTGTTACGAATTTC
1 ATTTTGTGTTACGAATTTC
*
229251 ATTTTCGTGTTGCGAATTT
1 ATTTT-GTGTTACGAATTT
229270 AAGTTTCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.18, C:0.11, G:0.18, T:0.53
Consensus pattern (19 bp):
ATTTTGTGTTACGAATTTC
Found at i:229276 original size:20 final size:20
Alignment explanation
Indices: 229237--229276 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
229227 TGCGAATTTT
* *
229237 GTGTTACGAATTTCATTTTC
1 GTGTTACGAATTTAAGTTTC
*
229257 GTGTTGCGAATTTAAGTTTC
1 GTGTTACGAATTTAAGTTTC
229277 AAAAACTACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (20 bp):
GTGTTACGAATTTAAGTTTC
Found at i:230805 original size:42 final size:42
Alignment explanation
Indices: 230746--230899 Score: 200
Period size: 42 Copynumber: 3.7 Consensus size: 42
230736 ATGAGCACCT
* * * **
230746 TCCACTTCGACACCGAGATCCATCACCTCATCGAGCCTCTTC
1 TCCACCTCGACACCGAGAGCCATCACCTGATCGAGCCAATTC
* * * * *
230788 TCCACTTCCACACCGAGATCCATCACCTGATCGAGTCGATTC
1 TCCACCTCGACACCGAGAGCCATCACCTGATCGAGCCAATTC
*
230830 TCCACCTCGACACCGAGAGCCATCACCTGATCTAGCCAATTC
1 TCCACCTCGACACCGAGAGCCATCACCTGATCGAGCCAATTC
*
230872 TCCACCTCGACACCGAGAGCCATAACCT
1 TCCACCTCGACACCGAGAGCCATCACCT
230900 ATTCCATCAC
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 100 1.00
ACGTcount: A:0.25, C:0.41, G:0.14, T:0.21
Consensus pattern (42 bp):
TCCACCTCGACACCGAGAGCCATCACCTGATCGAGCCAATTC
Found at i:231064 original size:21 final size:21
Alignment explanation
Indices: 231013--231147 Score: 123
Period size: 21 Copynumber: 6.4 Consensus size: 21
231003 AGTTATATGT
231013 TTTACGTGATGAGGTCA-GTGC
1 TTTACGTGATGAGGT-AGGTGC
** *
231034 TTTATATGATGAGGTCGGTGC
1 TTTACGTGATGAGGTAGGTGC
**
231055 TTTACGTGATGA-CAATGGTGC
1 TTTACGTGATGAGGTA-GGTGC
* **
231076 ATGGCGTGATGAGGTAGG-GTC
1 TTTACGTGATGAGGTAGGTG-C
* *
231097 TTTACGTGGTGAGGTAGTTGC
1 TTTACGTGATGAGGTAGGTGC
231118 TTTACGTGATGAGGTAGGTGC
1 TTTACGTGATGAGGTAGGTGC
*
231139 TCTACGTGA
1 TTTACGTGA
231148 GATTGTTTTA
Statistics
Matches: 88, Mismatches: 21, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.01
21 85 0.97
22 2 0.02
ACGTcount: A:0.19, C:0.12, G:0.36, T:0.33
Consensus pattern (21 bp):
TTTACGTGATGAGGTAGGTGC
Found at i:231457 original size:21 final size:21
Alignment explanation
Indices: 231431--231481 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
231421 GAAGAAGCTT
* *
231431 GATCCATCTACAATTTTTCAG
1 GATCCACCTACAATTGTTCAG
* *
231452 GATCCACCTCCCATTGTTCAG
1 GATCCACCTACAATTGTTCAG
*
231473 GATTCACCT
1 GATCCACCT
231482 TTCATCGTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (21 bp):
GATCCACCTACAATTGTTCAG
Found at i:231491 original size:21 final size:21
Alignment explanation
Indices: 231447--231561 Score: 110
Period size: 21 Copynumber: 5.6 Consensus size: 21
231437 TCTACAATTT
*
231447 TTCAGGATCCACCTCCCATTG
1 TTCAGGATCCACCTCCCATCG
* **
231468 TTCAGGATTCACCTTTCATCG
1 TTCAGGATCCACCTCCCATCG
* *
231489 TTCAAGAGGCC-CCTCCCATCG
1 TTCAGGA-TCCACCTCCCATCG
* **
231510 TTCAAGAGGC-CC-CCCATCG
1 TTCAGGATCCACCTCCCATCG
*
231529 TTCAGGATCCACCTCCCATCA
1 TTCAGGATCCACCTCCCATCG
231550 TTCAGGATCCAC
1 TTCAGGATCCAC
231562 ATTCCATACT
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
19 14 0.18
20 6 0.08
21 56 0.73
22 1 0.01
ACGTcount: A:0.21, C:0.38, G:0.16, T:0.25
Consensus pattern (21 bp):
TTCAGGATCCACCTCCCATCG
Found at i:231568 original size:21 final size:21
Alignment explanation
Indices: 231522--231568 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
231512 CAAGAGGCCC
* *
231522 CCCATCGTTCAGGATCCACCT
1 CCCATCATTCAGGATCCACAT
231543 CCCATCATTCAGGATCCACAT
1 CCCATCATTCAGGATCCACAT
*
231564 TCCAT
1 CCCAT
231569 ACTATGTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.40, G:0.11, T:0.26
Consensus pattern (21 bp):
CCCATCATTCAGGATCCACAT
Found at i:233799 original size:37 final size:37
Alignment explanation
Indices: 233746--233850 Score: 156
Period size: 37 Copynumber: 2.8 Consensus size: 37
233736 CCATTTCGTC
233746 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
233783 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
233820 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
233851 CCACAAGCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 60 1.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:234254 original size:2 final size:2
Alignment explanation
Indices: 234249--234301 Score: 83
Period size: 2 Copynumber: 27.5 Consensus size: 2
234239 TTAGTGTTAT
234249 TA TA TA TA TA TA T- 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
*
234290 TA T- TT TA TA TA T
1 TA TA TA TA TA TA T
234302 TTCCTATTTT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:239016 original size:16 final size:15
Alignment explanation
Indices: 238990--239035 Score: 67
Period size: 16 Copynumber: 3.1 Consensus size: 15
238980 AGATCCAATC
238990 AAGAACAAAAAAGAA
1 AAGAACAAAAAAGAA
239005 AAGAAGCAAAAAAGAA
1 AAGAA-CAAAAAAGAA
*
239021 AAGAA-AAAAGAGAA
1 AAGAACAAAAAAGAA
239035 A
1 A
239036 CAATAACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 9 0.31
15 5 0.17
16 15 0.52
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAACAAAAAAGAA
Found at i:240787 original size:106 final size:106
Alignment explanation
Indices: 240662--241725 Score: 1648
Period size: 106 Copynumber: 10.0 Consensus size: 106
240652 ATATCGTGCC
* * * * * * * * *
240662 ACTCGAGACAACACAAGTTCAACTTCACAACGAAAGGACGGTTGGTTGTCAACAAAAAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
* *
240727 AATTTCATAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
240768 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTGAATAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
*
240833 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
240874 ACTCCAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAATAAACAACTTCAT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTC-T
240939 -AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
240980 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
*
241045 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
241086 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
* *
241151 AATTTCAAAGCCAATTTCAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
241192 ACTCAAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
*
241257 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
241298 ACTCCAGACAAAGCAAGTTCAACTTCACGACGAAGCGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
* *
241363 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATGTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
241404 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAATAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
* * *
241469 AATTTCATAGTCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
241510 ACTCAAGACAACGAAAGTTCAACTTCACGATGAAGGGACTGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
* * *
241575 AATTTCATAGTCAATTTCGACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
241616 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
*
241681 AATTCCAGAGCCAATTTCAACTTCAC-GAC-AGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGA-AGGATATTGG
241722 ACTC
1 ACTC
241726 GGAACAATGC
Statistics
Matches: 884, Mismatches: 70, Indels: 8
0.92 0.07 0.01
Matches are distributed among these distances:
105 3 0.00
106 880 1.00
107 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCTC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:242511 original size:37 final size:37
Alignment explanation
Indices: 242445--242525 Score: 108
Period size: 37 Copynumber: 2.2 Consensus size: 37
242435 CTGTCAACAC
* *
242445 ATAGGATAGAATTTTGCTAGGATTCAAACTCCTAAAA
1 ATAGGATAGAATTCTACTAGGATTCAAACTCCTAAAA
* * * *
242482 ATAGGATAGAGTTCTACTATGATTTAAACTCCTAAAG
1 ATAGGATAGAATTCTACTAGGATTCAAACTCCTAAAA
242519 ATAGGAT
1 ATAGGAT
242526 CCACAAGCAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (37 bp):
ATAGGATAGAATTCTACTAGGATTCAAACTCCTAAAA
Found at i:243059 original size:20 final size:20
Alignment explanation
Indices: 243008--243068 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
242998 TGATTTTCTT
*
243008 TTTTTTTTATTATTATTTTAC
1 TTTTTTTTA-TATGATTTTAC
* * * *
243029 TTATATATATATGCTTTTAC
1 TTTTTTTTATATGATTTTAC
243049 TTTTTTTTATAT-ATTTTAC
1 TTTTTTTTATATGATTTTAC
243068 T
1 T
243069 CATTTGTTTA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
19 7 0.23
20 18 0.58
21 6 0.19
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTTTTTTATATGATTTTAC
Found at i:245974 original size:20 final size:20
Alignment explanation
Indices: 245949--245992 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
245939 GAACACGTTG
245949 GCATTGGTTAATGCATAGAT
1 GCATTGGTTAATGCATAGAT
245969 GCATTGGTTAATGCATAGAT
1 GCATTGGTTAATGCATAGAT
245989 GCAT
1 GCAT
245993 ATGTTTGGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (20 bp):
GCATTGGTTAATGCATAGAT
Found at i:252884 original size:19 final size:20
Alignment explanation
Indices: 252848--252891 Score: 65
Period size: 19 Copynumber: 2.2 Consensus size: 20
252838 AAATTTGGCG
252848 GTTTTTCCAGTTTTTTTCT-
1 GTTTTTCCAGTTTTTTTCTA
252867 GTTTTTCCTAG-TTTTTTCTA
1 GTTTTTCC-AGTTTTTTTCTA
252887 GTTTT
1 GTTTT
252892 CAGCTAGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.07, C:0.14, G:0.11, T:0.68
Consensus pattern (20 bp):
GTTTTTCCAGTTTTTTTCTA
Done.