Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007905.1 Hibiscus syriacus cultivar Beakdansim tig00110299_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: 2946335
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 14
Found at i:291337 original size:18 final size:18
Alignment explanation
Indices: 291306--291344 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
291296 TGAAGTTGGA
* *
291306 AAATGAAATAAAATATAG
1 AAATGAAAGAAAATAGAG
*
291324 AAATGAAAGGAAATAGAG
1 AAATGAAAGAAAATAGAG
291342 AAA
1 AAA
291345 AAAAAAAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (18 bp):
AAATGAAAGAAAATAGAG
Found at i:292331 original size:21 final size:21
Alignment explanation
Indices: 292305--292347 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
292295 CTATAGTTGA
292305 CCCCAAACTATTAAACTTGGT
1 CCCCAAACTATTAAACTTGGT
*
292326 CCCCAAACTGTTAAACTTGGT
1 CCCCAAACTATTAAACTTGGT
292347 C
1 C
292348 GCGAAGTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (21 bp):
CCCCAAACTATTAAACTTGGT
Found at i:296250 original size:35 final size:36
Alignment explanation
Indices: 296172--296243 Score: 110
Period size: 35 Copynumber: 2.0 Consensus size: 36
296162 TTCATGAATG
* * *
296172 TGTTACATGCATGGTATTTGTATCTGCATAAATGTA
1 TGTTGCATGCATGGTATGTGTATCTGAATAAATGTA
296208 TGTTGCATGCATGGTA-GTGTATCTGAATAAATGTA
1 TGTTGCATGCATGGTATGTGTATCTGAATAAATGTA
296243 T
1 T
296244 AGTGCATCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
35 18 0.55
36 15 0.45
ACGTcount: A:0.28, C:0.10, G:0.22, T:0.40
Consensus pattern (36 bp):
TGTTGCATGCATGGTATGTGTATCTGAATAAATGTA
Found at i:296332 original size:82 final size:81
Alignment explanation
Indices: 296203--296365 Score: 245
Period size: 82 Copynumber: 2.0 Consensus size: 81
296193 ATCTGCATAA
**
296203 ATGTATGTTGCATGCATGGTAGTGTATCTGAATAAATGTATAGTGCATCTTCATCCTCTGAATTT
1 ATGTATGTCACATGCATGGTAGTGTATCTGAATAAATGTATAGTGCATCTTCATCCTCTGAATTT
*
296268 GTATCATATAATAATT
66 GCATCATATAATAATT
* * * * *
296284 ATGTATGTCACATGCATGGTATTTGTATCTGCATTAATGTATATTGCATCTTCATGCTCTGAATT
1 ATGTATGTCACATGCATGGTA-GTGTATCTGAATAAATGTATAGTGCATCTTCATCCTCTGAATT
296349 TGCATCATATAATAATT
65 TGCATCATATAATAATT
296366 TTAATATATG
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
81 19 0.26
82 54 0.74
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (81 bp):
ATGTATGTCACATGCATGGTAGTGTATCTGAATAAATGTATAGTGCATCTTCATCCTCTGAATTT
GCATCATATAATAATT
Found at i:296389 original size:82 final size:82
Alignment explanation
Indices: 296225--296389 Score: 197
Period size: 82 Copynumber: 2.0 Consensus size: 82
296215 TGCATGGTAG
* *
296225 TGTATCTGAATAAATGTATAGTGCATCTTCATCCTCTGAATTTGTATCATATAATAATTATGTAT
1 TGTATCTGAATAAATGTATAGTGCATCTTCATCCTCTGAATTTGCATCATATAATAATTATATAT
* ***
296290 GTCACATGCATGGTATT
66 ATCACATGCAAAATATT
* * * * *
296307 TGTATCTGCATTAATGTATATTGCATCTTCATGCTCTGAATTTGCATCATATAATAATTTTAATA
1 TGTATCTGAATAAATGTATAGTGCATCTTCATCCTCTGAATTTGCATCATATAATAATTAT-ATA
* *
296372 TATGA-ATTCAAAATATT
65 TATCACATGCAAAATATT
296389 T
1 T
296390 AAATGCGAAA
Statistics
Matches: 69, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
82 64 0.93
83 5 0.07
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (82 bp):
TGTATCTGAATAAATGTATAGTGCATCTTCATCCTCTGAATTTGCATCATATAATAATTATATAT
ATCACATGCAAAATATT
Found at i:302144 original size:258 final size:253
Alignment explanation
Indices: 301644--302161 Score: 703
Period size: 258 Copynumber: 2.0 Consensus size: 253
301634 CCCCAGATAA
301644 GTCTCCCGCCTTCAAGTTTTCTTCATTGGTTTTGGTTGTTGTGCATGAAGGGTCTTCCCTTTTAG
1 GTCTCCCGCCTTCAAGTTTTCTTCATTGGTTTTGGTTGTTGT-CATGAAGGGTCTTCCCTTTTAG
* * * *
301709 CTGGAGTCGAGGGCTTGAGGATTCTTTTGCTTCTCTTTAAACTGGTATTTCACAATTCCTGGCTT
65 CTGGAGTCGAGGGCTTGAGGATTCTTTTGCTTCTCTCTAAACTGGGATTTCAAAACTCCTGGCTT
301774 GGAGGTGGTAAAGATTACATTTTGCTTCTTTTGTTTTTCCATTTTGGCATCTGGGTTTTAATGGT
130 GGAGGTGGTAAAGATTACA-------T-TTTTGTTTTTCCATTTTGGCATCTGGGTTTTAATGGT
* **
301839 TTGGTGTGCTTGAATTGGTTTCTGAATCTTCTGTTCATAGTAAAAGTTGCCAAAAGTTAGTTTTA
187 TTGGTGTGCTTGAACTGGTTTCTGAATCTTCTGTAAATAGTAAAAGTTGCCAAAAGTTAGTTTTA
301904 AG
252 AG
* *
301906 GTCTCCTGCCTTCAAGTTTTCTTCTTTGGTTTTGGTTGTT-T-ATGAA-GGTCTTCCCTTTTAGC
1 GTCTCCCGCCTTCAAGTTTTCTTCATTGGTTTTGGTTGTTGTCATGAAGGGTCTTCCCTTTTAGC
*
301968 TGGAGTTGAGGGCTTGAGGATTC-TTTGACTTCTCTCTAAACTGGGATTTCAAAACTCCTGGCTT
66 TGGAGTCGAGGGCTTGAGGATTCTTTTG-CTTCTCTCTAAACTGGGATTTCAAAACTCCTGGCTT
* *
302032 GGAGTTGGTAAAGATTACA-TTTT-TTTTT-CATTTTTGGTATCTGGGTTTTAATGGTTTGGTGT
130 GGAGGTGGTAAAGATTACATTTTTGTTTTTCCA-TTTTGGCATCTGGGTTTTAATGGTTTGGTGT
* * *
302094 GCTTGAACTGGTTTCTGAATC-TCT-TACTCATAGTAAAAGTTGTCAAAAGTTGGTGTTTTAAG
194 GCTTGAACTGGTTTCTGAATCTTCTGTA--AATAGTAAAAGTTGCCAAAAGTT--AGTTTTAAG
302156 GTCTCC
1 GTCTCC
302162 TGGGAATTAA
Statistics
Matches: 237, Mismatches: 13, Indels: 24
0.86 0.05 0.09
Matches are distributed among these distances:
246 1 0.00
247 5 0.02
248 77 0.32
249 4 0.02
250 14 0.06
257 4 0.02
258 88 0.37
259 5 0.02
261 1 0.00
262 38 0.16
ACGTcount: A:0.18, C:0.15, G:0.23, T:0.44
Consensus pattern (253 bp):
GTCTCCCGCCTTCAAGTTTTCTTCATTGGTTTTGGTTGTTGTCATGAAGGGTCTTCCCTTTTAGC
TGGAGTCGAGGGCTTGAGGATTCTTTTGCTTCTCTCTAAACTGGGATTTCAAAACTCCTGGCTTG
GAGGTGGTAAAGATTACATTTTTGTTTTTCCATTTTGGCATCTGGGTTTTAATGGTTTGGTGTGC
TTGAACTGGTTTCTGAATCTTCTGTAAATAGTAAAAGTTGCCAAAAGTTAGTTTTAAG
Found at i:303221 original size:159 final size:156
Alignment explanation
Indices: 302946--303255 Score: 469
Period size: 159 Copynumber: 2.0 Consensus size: 156
302936 AAGAATACGC
* * *
302946 TGAACCACCAAGTGCTTCACAAATTCCGAAAGTTGTCAAGGAGAAAACCAAGAACAAGAAGATCA
1 TGAACCACCAAATGCTTCACAAAATCCGAAAGTTGTCAAAGAGAAAACCAAGAACAAGAAGATCA
* * * *
303011 GTGAAGCTCGAGATAACAAGGTTGTGGATCAAATTGAGGAGAAGAAGGTTGATGAAAATGTAGAG
66 GTGAAGCTCAAGATAACAAGGTTGTGAATCAAATTGAGGAGAAGAAAGTTGATAAAAATGTAGAG
303076 GAAAAGAAGGCTGAGGATAAATATGT
131 GAAAAGAAGGCTGAGGATAAATATGT
* *
303102 TGAACCACCAAATGCTTCCCAAACAT-CGAAAGTTGTCAAAGAGAAAACCAAGAAGAAGAAGAAA
1 TGAACCACCAAATGCTTCACAAA-ATCCGAAAGTTGTCAAAGAGAAAACCAAGAACAAGAAG---
* * *
303166 ATCAGTGAAGCTCAAGATGACAAGGTTGTTAATCGAATTGAGGAGAAGAAAGTTGATAAAAATGT
62 ATCAGTGAAGCTCAAGATAACAAGGTTGTGAATCAAATTGAGGAGAAGAAAGTTGATAAAAATGT
303231 AGAGGAAAAGAAGGCTGAGGATAAA
127 AGAGGAAAAGAAGGCTGAGGATAAA
303256 CAGGTTGTGG
Statistics
Matches: 138, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
156 54 0.39
157 1 0.01
159 83 0.60
ACGTcount: A:0.45, C:0.12, G:0.25, T:0.18
Consensus pattern (156 bp):
TGAACCACCAAATGCTTCACAAAATCCGAAAGTTGTCAAAGAGAAAACCAAGAACAAGAAGATCA
GTGAAGCTCAAGATAACAAGGTTGTGAATCAAATTGAGGAGAAGAAAGTTGATAAAAATGTAGAG
GAAAAGAAGGCTGAGGATAAATATGT
Found at i:311025 original size:20 final size:19
Alignment explanation
Indices: 310993--311032 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
310983 TTGTGAACTT
310993 GCAAAACTCAAAACAACAAA
1 GCAAAACTCAAAACAA-AAA
311013 GCAAAAC-CAAAAACAAAAA
1 GCAAAACTC-AAAACAAAAA
311032 G
1 G
311033 AACCCATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.68, C:0.23, G:0.07, T:0.03
Consensus pattern (19 bp):
GCAAAACTCAAAACAAAAA
Found at i:313510 original size:15 final size:15
Alignment explanation
Indices: 313492--313524 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
313482 GTGAATATAG
313492 AAAATACAAGATTTT
1 AAAATACAAGATTTT
313507 AAAATACAAGATTTT
1 AAAATACAAGATTTT
313522 AAA
1 AAA
313525 TTAGAGGTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.30
Consensus pattern (15 bp):
AAAATACAAGATTTT
Found at i:313778 original size:2 final size:2
Alignment explanation
Indices: 313771--313817 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
313761 GTCTCCACTT
313771 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
313813 TA TA T
1 TA TA T
313818 CGAGTTTCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:317656 original size:17 final size:17
Alignment explanation
Indices: 317634--317719 Score: 117
Period size: 17 Copynumber: 5.2 Consensus size: 17
317624 GACCGGTCAC
**
317634 GACCCGACCCGATAGTT
1 GACCCGACCCGACCGTT
317651 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
317668 GACCCGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
317686 GACCCGA--C--CCGTT
1 GACCCGACCCGACCGTT
317699 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
317716 GACC
1 GACC
317720 GTTGACCGTT
Statistics
Matches: 62, Mismatches: 2, Indels: 10
0.84 0.03 0.14
Matches are distributed among these distances:
13 12 0.19
15 1 0.02
16 1 0.02
17 36 0.58
18 12 0.19
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:317658 original size:22 final size:19
Alignment explanation
Indices: 317633--317696 Score: 80
Period size: 18 Copynumber: 3.4 Consensus size: 19
317623 TGACCGGTCA
317633 CGACCCGACCCGATAGTTGACC
1 CGACCCGACCCG---GTTGACC
317655 CGACCCGA-CC-GTTGACC
1 CGACCCGACCCGGTTGACC
317672 CGACCCGACCC-GTTGACC
1 CGACCCGACCCGGTTGACC
317690 CGACCCG
1 CGACCCG
317697 TTGACCCGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
17 15 0.37
18 16 0.39
21 2 0.05
22 8 0.20
ACGTcount: A:0.19, C:0.47, G:0.23, T:0.11
Consensus pattern (19 bp):
CGACCCGACCCGGTTGACC
Found at i:317691 original size:13 final size:13
Alignment explanation
Indices: 317673--317709 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
317663 CCGTTGACCC
317673 GACCCGACCCGTT
1 GACCCGACCCGTT
317686 GACCCGACCCGTT
1 GACCCGACCCGTT
317699 GACCCGACCCG
1 GACCCGACCCG
317710 ACCGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:317721 original size:7 final size:7
Alignment explanation
Indices: 317709--317741 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
317699 GACCCGACCC
317709 GACCGTT
1 GACCGTT
317716 GACCGTT
1 GACCGTT
317723 GACCGTT
1 GACCGTT
317730 GACCGTT
1 GACCGTT
317737 GACCG
1 GACCG
317742 GTGCTATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (7 bp):
GACCGTT
Found at i:317729 original size:31 final size:30
Alignment explanation
Indices: 317656--317733 Score: 113
Period size: 31 Copynumber: 2.5 Consensus size: 30
317646 TAGTTGACCC
317656 GACCCGACCGTTGACCCGACCCGACCCGTT
1 GACCCGACCGTTGACCCGACCCGACCCGTT
317686 GACCCGACCCGTTGACCCGACCCGA-CCGTT
1 GACCCGA-CCGTTGACCCGACCCGACCCGTT
*
317716 GACCGTTGACCGTTGACC
1 GACC--CGACCGTTGACC
317734 GTTGACCGGT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
30 16 0.36
31 26 0.59
32 2 0.05
ACGTcount: A:0.17, C:0.44, G:0.24, T:0.15
Consensus pattern (30 bp):
GACCCGACCGTTGACCCGACCCGACCCGTT
Found at i:317783 original size:29 final size:29
Alignment explanation
Indices: 317741--317822 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
317731 ACCGTTGACC
*
317741 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
317770 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
317799 GGTGCTATTCTGGTAAATAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
317823 AAAAAGGGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:317835 original size:30 final size:29
Alignment explanation
Indices: 317770--317845 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
317760 ATTCGGTTTT
*****
317770 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAAAAAG
317799 GGTGCTATTCTGGTAAATAATTCGAAAAAG
1 GGTGCTATTCTGGTAAATAATTC-AAAAAG
317829 GGTGCTATT-TGTGTAAA
1 GGTGCTATTCTG-GTAAA
317846 ATGTTCAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAAAAAG
Found at i:324944 original size:17 final size:17
Alignment explanation
Indices: 324922--324994 Score: 119
Period size: 17 Copynumber: 4.2 Consensus size: 17
324912 GACCGGTCAC
**
324922 GACCCGACCCGATAGTT
1 GACCCGACCCGACCGTT
324939 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
324956 GACCCGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
324974 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
324991 GACC
1 GACC
324995 GTTGACCGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
17 36 0.68
18 17 0.32
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.12
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:324982 original size:35 final size:34
Alignment explanation
Indices: 324922--324994 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 34
324912 GACCGGTCAC
*
324922 GACCCGACCCGATAGTTGACCCGACCCGACCGTT
1 GACCCGACCCGACAGTTGACCCGACCCGACCGTT
*
324956 GACCCGACCCGACCCGTTGACCCGACCCGACCGTT
1 GACCCGACCCGA-CAGTTGACCCGACCCGACCGTT
324991 GACC
1 GACC
324995 GTTGACCGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
34 12 0.33
35 24 0.67
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.12
Consensus pattern (34 bp):
GACCCGACCCGACAGTTGACCCGACCCGACCGTT
Found at i:324996 original size:7 final size:7
Alignment explanation
Indices: 324984--325023 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
324974 GACCCGACCC
324984 GACCGTT
1 GACCGTT
324991 GACCGTT
1 GACCGTT
324998 GACCGTT
1 GACCGTT
325005 GACCGTT
1 GACCGTT
325012 GACCGTT
1 GACCGTT
325019 GACCG
1 GACCG
325024 GTGCTATTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (7 bp):
GACCGTT
Found at i:325065 original size:29 final size:29
Alignment explanation
Indices: 325023--325104 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
325013 ACCGTTGACC
*
325023 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
325052 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
325081 GGTGCTATTCTGGTAAATAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
325105 AAAAAGGGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.44
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:325117 original size:30 final size:29
Alignment explanation
Indices: 325052--325127 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
325042 ATTCGGTTTT
*****
325052 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAAAAAG
325081 GGTGCTATTCTGGTAAATAATTCGAAAAAG
1 GGTGCTATTCTGGTAAATAATTC-AAAAAG
325111 GGTGCTATT-TGTGTAAA
1 GGTGCTATTCTG-GTAAA
325128 ATGTTCAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAAAAAG
Found at i:328078 original size:18 final size:16
Alignment explanation
Indices: 328055--328097 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
328045 AGCAAATCAC
328055 TCTCTCTCTCTATCTCT
1 TCTCTCTCTCTATCT-T
328072 ATCTCTCTGC-CTATCTT
1 -TCTCTCT-CTCTATCTT
328089 TCTCTCTCT
1 TCTCTCTCT
328098 ACGAGAGATG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 1 0.04
16 7 0.30
17 1 0.04
18 13 0.57
19 1 0.04
ACGTcount: A:0.07, C:0.40, G:0.02, T:0.51
Consensus pattern (16 bp):
TCTCTCTCTCTATCTT
Found at i:328877 original size:21 final size:24
Alignment explanation
Indices: 328851--328912 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 24
328841 TCACAAAATT
*
328851 ATAATTTTAAAAAATATT-TT-TC
1 ATAATTTTAAAAAAAATTATTATC
328873 A-AATTTTAAAAATAAATTATTATC
1 ATAATTTTAAAAA-AAATTATTATC
328897 ATATATTTTAAAAAAA
1 ATA-ATTTTAAAAAAA
328913 CTGAATTATC
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
21 11 0.32
22 5 0.15
23 2 0.06
24 3 0.09
25 3 0.09
26 10 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
ATAATTTTAAAAAAAATTATTATC
Found at i:331654 original size:19 final size:19
Alignment explanation
Indices: 331618--331654 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
331608 AGAATTTAAA
* *
331618 TTTTTTTTAAATATAATAT
1 TTTTTTTTAAAAAAAATAT
331637 TTTTTTTTAAAAAAAATA
1 TTTTTTTTAAAAAAAATA
331655 AAATTTTTAA
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TTTTTTTTAAAAAAAATAT
Found at i:333785 original size:2 final size:2
Alignment explanation
Indices: 333778--333842 Score: 103
Period size: 2 Copynumber: 32.0 Consensus size: 2
333768 TAATTTGAGA
333778 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
* *
333820 AT AT AT CT CAA AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT AT AT AT
333843 TGGTAAGGTA
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:339145 original size:2 final size:2
Alignment explanation
Indices: 339138--339169 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
339128 AATTGTTTGC
339138 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
339170 TAATACCTAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:339512 original size:55 final size:54
Alignment explanation
Indices: 339418--339575 Score: 196
Period size: 55 Copynumber: 2.9 Consensus size: 54
339408 ATATTCGGAA
*
339418 AACGAGTTCGCTCCCTCATTT-TTAGGGAGTATAGAACTCGAACAATTTTCTG-C
1 AACGAGTTCGCTCCCTC-TTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
* *
339471 GAACGAGTTCACTCCCTCTTTCTTCGGGGAGTATAGAACTCGAACAATCTTCTGTC
1 -AACGAGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAACAATCTTCTGTC
* * * * *
339527 AACGGGTTCGTTCCCTCTTTCTTAGGGAGTA-GGAACTTGAAGAATCTTC
1 AACGAGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTC
339576 ATCAATCGTG
Statistics
Matches: 91, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
53 18 0.20
54 25 0.27
55 47 0.52
56 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (54 bp):
AACGAGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAACAATCTTCTGTC
Found at i:339963 original size:55 final size:55
Alignment explanation
Indices: 339569--339963 Score: 592
Period size: 55 Copynumber: 7.2 Consensus size: 55
339559 GAACTTGAAG
* * * *
339569 AATCTTCATCAATCGTGTCTGCTCCCTATTTCCTCAGAGAGTATAAGACCCAAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
339624 AATCTTCAACAAATCCTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACCCAAAC
1 AATCTTCAAC-AATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * *
339680 AATCTTCATCAATCGTGTCTGCTCCCCATTCCTTCAGAGAGTATAAGACTTGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * *
339735 AATCTTCATCAATCGTGTCTGCTCCCTATTCCTTCAGAGAGTACAAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* * * *
339790 AATCTTCATCCATCGTGTCTGCTCCATATTTCTGCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
*
339845 AATTTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
* *
339900 AATCTTCAACAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATC
1 AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
339955 AATCTTCAA
1 AATCTTCAA
339964 TTATCGTTGG
Statistics
Matches: 313, Mismatches: 26, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
55 261 0.83
56 52 0.17
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.30
Consensus pattern (55 bp):
AATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAC
Found at i:340986 original size:16 final size:16
Alignment explanation
Indices: 340965--341016 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
340955 GAACCCTTCT
*
340965 TTTTTTCCATTTTTCA
1 TTTTTTCAATTTTTCA
* *
340981 TTTTTTTAATTTTTTA
1 TTTTTTCAATTTTTCA
* * *
340997 TTTTTTTATTTTTTTA
1 TTTTTTCAATTTTTCA
341013 TTTT
1 TTTT
341017 CACTCATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTTTCAATTTTTCA
Found at i:354785 original size:53 final size:52
Alignment explanation
Indices: 354695--354796 Score: 150
Period size: 53 Copynumber: 1.9 Consensus size: 52
354685 CTTAAATCCC
*
354695 AAATCAGAGAAGTTTAGGATACTAACCATGAAAGAAAAGCGAGAATGAAGCA
1 AAATCAGAGAAGATTAGGATACTAACCATGAAAGAAAAGCGAGAATGAAGCA
* * * *
354747 AAATCAAGAGAAGATTAGGGTACTTACCCTGAACGAAAAGCGAGAATGAA
1 AAATC-AGAGAAGATTAGGATACTAACCATGAAAGAAAAGCGAGAATGAA
354797 AATGGAAGAG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
52 5 0.11
53 39 0.89
ACGTcount: A:0.48, C:0.13, G:0.24, T:0.16
Consensus pattern (52 bp):
AAATCAGAGAAGATTAGGATACTAACCATGAAAGAAAAGCGAGAATGAAGCA
Found at i:356790 original size:15 final size:15
Alignment explanation
Indices: 356768--356850 Score: 98
Period size: 15 Copynumber: 5.5 Consensus size: 15
356758 GGGTACGGTT
356768 AAGAAGAAAGAAAGG
1 AAGAAGAAAGAAAGG
**
356783 GTGAAGAAAGAAAGG
1 AAGAAGAAAGAAAGG
356798 AAGAAGAAAGAAAGG
1 AAGAAGAAAGAAAGG
*
356813 AAAGGAAG-AAGAAATG
1 -AA-GAAGAAAGAAAGG
356829 AAGAAG-AAGAAAGG
1 AAGAAGAAAGAAAGG
*
356843 GAGAAGAA
1 AAGAAGAA
356851 GAGATCGAGT
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
14 16 0.28
15 29 0.50
16 9 0.16
17 4 0.07
ACGTcount: A:0.63, C:0.00, G:0.35, T:0.02
Consensus pattern (15 bp):
AAGAAGAAAGAAAGG
Found at i:356804 original size:11 final size:11
Alignment explanation
Indices: 356785--356850 Score: 64
Period size: 11 Copynumber: 5.8 Consensus size: 11
356775 AAGAAAGGGT
356785 GAAGAAAGAAAG
1 GAAG-AAGAAAG
356797 GAAGAAGAAA-
1 GAAGAAGAAAG
*
356807 GAA-AGGAAAG
1 GAAGAAGAAAG
356817 GAAGAAGAAATG
1 GAAGAAGAAA-G
356829 AAGAAGAAGAAAG
1 --GAAGAAGAAAG
*
356842 GGAGAAGAA
1 GAAGAAGAA
356851 GAGATCGAGT
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
9 5 0.11
10 6 0.13
11 19 0.41
12 5 0.11
13 1 0.02
14 10 0.22
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.02
Consensus pattern (11 bp):
GAAGAAGAAAG
Found at i:356817 original size:20 final size:19
Alignment explanation
Indices: 356786--356826 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
356776 AGAAAGGGTG
356786 AAGAAAGAAAGGAAGAAGA
1 AAGAAAGAAAGGAAGAAGA
356805 AAGAAAGGAAAGGAAGAAGA
1 AAGAAA-GAAAGGAAGAAGA
356825 AA
1 AA
356827 TGAAGAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (19 bp):
AAGAAAGAAAGGAAGAAGA
Found at i:356925 original size:28 final size:30
Alignment explanation
Indices: 356889--356951 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
356879 TAGTTTAAAT
356889 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
356917 TATTAGTTTGTTAGTTTAAGTTATATATTA
1 TATTAGTTTGTTAGTTTAAGTTATATATTA
356947 TATTA
1 TATTA
356952 TATTATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 20 0.61
29 1 0.03
30 12 0.36
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (30 bp):
TATTAGTTTGTTAGTTTAAGTTATATATTA
Found at i:357712 original size:20 final size:20
Alignment explanation
Indices: 357645--357718 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 20
357635 AAACCATTAG
* *
357645 ATTAATAATAATTATTAAATC
1 ATTATTAATAA-TATTAAATA
* *
357666 ATTATTAGTAATATT-AGTA
1 ATTATTAATAATATTAAATA
* *
357685 ATCAATTAATCATATTAAATA
1 AT-TATTAATAATATTAAATA
*
357706 ATTATTAGTAATA
1 ATTATTAATAATA
357719 ATATTAAAGC
Statistics
Matches: 40, Mismatches: 11, Indels: 5
0.71 0.20 0.09
Matches are distributed among these distances:
19 4 0.10
20 22 0.55
21 14 0.35
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (20 bp):
ATTATTAATAATATTAAATA
Found at i:359674 original size:23 final size:23
Alignment explanation
Indices: 359648--359725 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
359638 CACCACAGCT
359648 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* * * *
359671 CATATAATTGCATCGGAGTACCG
1 CATATAATTGCACCGAAGTGCCA
* * *
359694 CATAGAATTGCACTGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
359717 TATAATAAT
1 CAT-ATAAT
359726 GTCCATAAGG
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 38 0.90
24 4 0.10
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.27
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:359903 original size:103 final size:103
Alignment explanation
Indices: 359732--359949 Score: 427
Period size: 103 Copynumber: 2.1 Consensus size: 103
359722 TAATGTCCAT
359732 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
359797 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
359835 AATGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
359900 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
359938 AAGGACCACATA
1 AAGGACCACATA
359950 GACCCTCGAC
Statistics
Matches: 113, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 113 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:361378 original size:21 final size:21
Alignment explanation
Indices: 361327--361378 Score: 88
Period size: 20 Copynumber: 2.5 Consensus size: 21
361317 AGGGGTATCA
361327 ATTCCCCATTGAATGGGTACCG
1 ATTCCCC-TTGAATGGGTACCG
361349 ATT-CCCTTGAATGGGTACCG
1 ATTCCCCTTGAATGGGTACCG
361369 ATTCCCCTTG
1 ATTCCCCTTG
361379 CCCATAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.59
21 9 0.31
22 3 0.10
ACGTcount: A:0.19, C:0.29, G:0.21, T:0.31
Consensus pattern (21 bp):
ATTCCCCTTGAATGGGTACCG
Found at i:365094 original size:11 final size:11
Alignment explanation
Indices: 365078--365119 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
365068 ACTCAACAAA
*
365078 TTATTTTTATT
1 TTATTTATATT
365089 TTATTTATATT
1 TTATTTATATT
*
365100 TTATGTAT-TT
1 TTATTTATATT
365110 ATTATTTATA
1 -TTATTTATA
365120 AATAGTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
10 2 0.08
11 24 0.92
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (11 bp):
TTATTTATATT
Found at i:365207 original size:16 final size:16
Alignment explanation
Indices: 365186--365243 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
365176 CCTTATTATT
365186 ATTTATAAATAGTCGA
1 ATTTATAAATAGTCGA
* *
365202 ATTTATTCAATTTAAATCGA
1 ATTTA-T-AA-AT-AGTCGA
*
365222 ATTTATAAATAGTTGA
1 ATTTATAAATAGTCGA
365238 ATTTAT
1 ATTTAT
365244 TATTTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 15 0.45
17 2 0.06
18 4 0.12
19 2 0.06
20 10 0.30
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (16 bp):
ATTTATAAATAGTCGA
Found at i:365207 original size:23 final size:22
Alignment explanation
Indices: 365181--365267 Score: 66
Period size: 23 Copynumber: 4.2 Consensus size: 22
365171 TTTTACCTTA
365181 TTATTATTTATAAATAGTCGAAT
1 TTATTATTTAT-AATAGTCGAAT
*
365204 TTATTCAATT-TAA-A-TCGAA-
1 TTATT-ATTTATAATAGTCGAAT
*
365223 -T-TTA--TA-AATAGTTGAAT
1 TTATTATTTATAATAGTCGAAT
365240 TTATTATTTATAAATAGTCGAAT
1 TTATTATTTAT-AATAGTCGAAT
365263 TTATT
1 TTATT
365268 CTTTTTACAT
Statistics
Matches: 50, Mismatches: 3, Indels: 22
0.67 0.04 0.29
Matches are distributed among these distances:
14 3 0.06
15 1 0.02
16 5 0.10
17 2 0.04
18 2 0.04
19 3 0.06
20 5 0.10
21 3 0.06
22 2 0.04
23 21 0.42
24 3 0.06
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.48
Consensus pattern (22 bp):
TTATTATTTATAATAGTCGAAT
Found at i:365329 original size:17 final size:15
Alignment explanation
Indices: 365295--365334 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
365285 GGAGGCATGC
365295 ATATTTAATATTATA
1 ATATTTAATATTATA
*
365310 ATATTTAAGTTTTAATA
1 ATATTTAA-TATT-ATA
365327 ATATTTAA
1 ATATTTAA
365335 CATATTTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 3 0.14
17 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (15 bp):
ATATTTAATATTATA
Found at i:367762 original size:57 final size:56
Alignment explanation
Indices: 367690--367797 Score: 139
Period size: 57 Copynumber: 1.9 Consensus size: 56
367680 TAACTTAAAC
* *
367690 TAATAAACT-ATTTTTTTATTATAATCCAACTT-AACTTAAACTAACAAACTAAAAAAT
1 TAATAAACTAATTTTTTTA-TATAATACAACTTCAAC--AAACAAACAAACTAAAAAAT
* *
367747 TAATTAACTAATTTTTTTATATAATATAACTTCAACAAACAAACAAACTAA
1 TAATAAACTAATTTTTTTATATAATACAACTTCAACAAACAAACAAACTAA
367798 CTAATATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
56 14 0.31
57 19 0.42
58 12 0.27
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (56 bp):
TAATAAACTAATTTTTTTATATAATACAACTTCAACAAACAAACAAACTAAAAAAT
Found at i:368098 original size:15 final size:14
Alignment explanation
Indices: 368071--368126 Score: 67
Period size: 15 Copynumber: 3.8 Consensus size: 14
368061 TTACGTACCC
368071 TTCTTCTTCTTTCT
1 TTCTTCTTCTTTCT
368085 TTCTTCTATCTTTCT
1 TTCTTCT-TCTTTCT
**
368100 TTCTTCCTTCTACCT
1 TTCTT-CTTCTTTCT
368115 TTCTTTCTTCTT
1 TTC-TTCTTCTT
368127 ACAACCGAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.19
15 25 0.69
16 4 0.11
ACGTcount: A:0.04, C:0.30, G:0.00, T:0.66
Consensus pattern (14 bp):
TTCTTCTTCTTTCT
Found at i:368101 original size:19 final size:19
Alignment explanation
Indices: 368077--368124 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
368067 ACCCTTCTTC
* *
368077 TTCTTTCTTTCTTCTATCT
1 TTCTTTCTTCCTTCTACCT
368096 TTCTTTCTTCCTTCTACCT
1 TTCTTTCTTCCTTCTACCT
368115 TTCTTTCTTC
1 TTCTTTCTTC
368125 TTACAACCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (19 bp):
TTCTTTCTTCCTTCTACCT
Found at i:368321 original size:30 final size:29
Alignment explanation
Indices: 368284--368368 Score: 75
Period size: 30 Copynumber: 2.9 Consensus size: 29
368274 GAAACAACCT
368284 TGGTCGCTAGGATTGCATGGCGACCTGCACA
1 TGGTCGCTAGGATTGCATGGCGACCT-C-CA
* * * * *
368315 -GGTCGCTCGGACTACACGACGACCTCCA
1 TGGTCGCTAGGATTGCATGGCGACCTCCA
*
368343 TGGTCGC-ATGGATTGCTTGGCGACCT
1 TGGTCGCTA-GGATTGCATGGCGACCT
368369 AGCTGCATGG
Statistics
Matches: 41, Mismatches: 11, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
28 2 0.05
29 19 0.46
30 20 0.49
ACGTcount: A:0.18, C:0.29, G:0.31, T:0.22
Consensus pattern (29 bp):
TGGTCGCTAGGATTGCATGGCGACCTCCA
Found at i:372237 original size:21 final size:21
Alignment explanation
Indices: 372207--372247 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
372197 GAAATGTTAA
* *
372207 AAACATTAATGTTTTAGGTAG
1 AAACAATAATATTTTAGGTAG
372228 AAACAATAATATTTTAGGTA
1 AAACAATAATATTTTAGGTA
372248 ATTTTTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (21 bp):
AAACAATAATATTTTAGGTAG
Found at i:374968 original size:15 final size:16
Alignment explanation
Indices: 374941--374972 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
374931 TATAAGTATA
374941 AGATTATATGATAATG
1 AGATTATATGATAATG
374957 AGATTA-ATGATAATG
1 AGATTATATGATAATG
374972 A
1 A
374973 AAGATTATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.19, T:0.34
Consensus pattern (16 bp):
AGATTATATGATAATG
Found at i:382741 original size:18 final size:18
Alignment explanation
Indices: 382707--382751 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
382697 TGATATTCGA
382707 ATAATTT-AATCGAATAT
1 ATAATTTAAATCGAATAT
*
382724 ATAATTTAAATTGAATAT
1 ATAATTTAAATCGAATAT
382742 A-AATCTTAAA
1 ATAAT-TTAAA
382752 ATTCAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (18 bp):
ATAATTTAAATCGAATAT
Found at i:382863 original size:11 final size:13
Alignment explanation
Indices: 382844--382875 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
382834 AGTATTTTAA
382844 TTGAAAATC-ATT
1 TTGAAAATCAATT
382856 TT-AAAATCAATT
1 TTGAAAATCAATT
382868 TTGAAAAT
1 TTGAAAAT
382876 TACTCCCCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 6 0.33
12 7 0.39
13 5 0.28
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (13 bp):
TTGAAAATCAATT
Found at i:384611 original size:18 final size:19
Alignment explanation
Indices: 384575--384620 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 19
384565 TATATAGTTT
384575 TCAAAACAAACATAATTAAA
1 TCAAAAC-AACATAATTAAA
384595 TCAAAACAACA-AATTAAA
1 TCAAAACAACATAATTAAA
*
384613 ACAAAACA
1 TCAAAACA
384621 TTTTTTTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 14 0.56
19 4 0.16
20 7 0.28
ACGTcount: A:0.67, C:0.17, G:0.00, T:0.15
Consensus pattern (19 bp):
TCAAAACAACATAATTAAA
Found at i:385116 original size:14 final size:14
Alignment explanation
Indices: 385097--385124 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
385087 CATAGCAAAG
385097 GGGTATCGATACCT
1 GGGTATCGATACCT
385111 GGGTATCGATACCT
1 GGGTATCGATACCT
385125 TGAGCACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (14 bp):
GGGTATCGATACCT
Found at i:390551 original size:17 final size:18
Alignment explanation
Indices: 390529--390575 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
390519 TTTATATTGA
390529 ATAATTT-AATTGAATAT
1 ATAATTTAAATTGAATAT
390546 ATAATTTAAAATTGAATAT
1 ATAATTT-AAATTGAATAT
*
390565 AAAATCTTAAA
1 ATAAT-TTAAA
390576 ATTCAATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
17 7 0.27
19 17 0.65
20 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.40
Consensus pattern (18 bp):
ATAATTTAAATTGAATAT
Found at i:390560 original size:19 final size:20
Alignment explanation
Indices: 390536--390583 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
390526 TGAATAATTT
*
390536 AATTGAATATATAAT-TTAA
1 AATTGAATATAAAATCTTAA
390555 AATTGAATATAAAATCTTAA
1 AATTGAATATAAAATCTTAA
*
390575 AATTCAATA
1 AATTGAATA
390584 ATACTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.54
20 12 0.46
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (20 bp):
AATTGAATATAAAATCTTAA
Found at i:391966 original size:25 final size:25
Alignment explanation
Indices: 391916--391969 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
391906 TCAAGGGTTC
*
391916 TATGTGGTCCTTCGGGCATATATTA
1 TATGTGGTCCTTCGAGCATATATTA
*
391941 TATGTGGTCCTTCGAG-ATAATTTTA
1 TATGTGGTCCTTCGAGCAT-ATATTA
391966 TATG
1 TATG
391970 CCCCTAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 24 0.92
ACGTcount: A:0.22, C:0.13, G:0.22, T:0.43
Consensus pattern (25 bp):
TATGTGGTCCTTCGAGCATATATTA
Found at i:393941 original size:23 final size:23
Alignment explanation
Indices: 393915--393962 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
393905 ATAAAGTACA
*
393915 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
*
393938 ATAATATAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
393961 AT
1 AT
393963 TTACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:394465 original size:23 final size:22
Alignment explanation
Indices: 394425--394499 Score: 84
Period size: 23 Copynumber: 3.5 Consensus size: 22
394415 GATAGATACT
*
394425 TTACA-ATATAAGCACTACCTA
1 TTACATATATAAGCGCTACCTA
* *
394446 TTACATTATATAAACGCTACTTA
1 TTACA-TATATAAGCGCTACCTA
394469 TTAC--ATATAAGCGCTACCTA
1 TTACATATATAAGCGCTACCTA
394489 TTACATCATAT
1 TTACAT-ATAT
394500 TTTTACCTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
20 18 0.41
21 5 0.11
23 21 0.48
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (22 bp):
TTACATATATAAGCGCTACCTA
Found at i:394478 original size:20 final size:20
Alignment explanation
Indices: 394425--394494 Score: 68
Period size: 20 Copynumber: 3.3 Consensus size: 20
394415 GATAGATACT
* *
394425 TTACAATATAAGCACTACCTA
1 TTAC-ATATAAACGCTACCTA
*
394446 TTACATTATATAAACGCTACTTA
1 TTAC---ATATAAACGCTACCTA
*
394469 TTACATATAAGCGCTACCTA
1 TTACATATAAACGCTACCTA
394489 TTACAT
1 TTACAT
394495 CATATTTTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
20 20 0.49
21 4 0.10
23 17 0.41
ACGTcount: A:0.39, C:0.21, G:0.06, T:0.34
Consensus pattern (20 bp):
TTACATATAAACGCTACCTA
Found at i:394868 original size:425 final size:429
Alignment explanation
Indices: 394268--395980 Score: 2941
Period size: 425 Copynumber: 4.0 Consensus size: 429
394258 ATGTTTATTG
* *
394268 TTTTTAATTTAATAATAATATATATTGTATCGT-AAAAAT-AATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAAT-ATATATATCGTAACGTGAAAAATAAATCATTAGACGCCTATAATTACT
394331 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTG-AAAAAG
65 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
*
394395 TATGGACACTTTTAT-AAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
130 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
* *
394459 ACGCTACTTATTAC-ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTG
195 ACGATACCTATTACTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTG
*
394523 TCCATACTTTTTATAAAAATGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA-TTTT
260 TCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTT
394587 TTTTAATAGTGTTTCATGTTTTCCACCTACAATATTTAATTTAATAATTTCATTTGCACAAAAAA
325 TTTTAATAGTGTTTCATGTTTTCCACCTACAATA-TTAATTTAATAATTTCATTTGCACAAAAAA
394652 TTATTTGATTGTTTTGATATTTTATAAAAT-ATATTTAGAA
389 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
*
394692 TTTTTAATTTAATAATATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTA
1 TTTTTAATTTAATAATATATATATCGTAACGTGAAAAATAAATCATTAGACGCCTATAATTACTA
*
394757 AATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCAACAGTGAAAAAAGT
66 AATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGT
*
394822 ATAGACACTTTTATAAAAAGGATAGATACTTTAC-A-ATAACCACTACCTATTACATTATATAAA
131 ATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAA
394885 CGATACCTATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTA-TATATTGAAAGT
196 CGATACCTATTAC--TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGT
394949 GTCCATAC-TTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAA---T
259 GTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTT
395010 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
324 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
395075 --ATTTGATTGTTTTGATATTTTATAAAA-AATATTTAGAA
389 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
*
395113 TTTTT-ATTTAAT-A-ATATATATCGTAACGTGAAAAATAAATCATTAGACACCTATAATTACTA
1 TTTTTAATTTAATAATATATATATCGTAACGTGAAAAATAAATCATTAGACGCCTATAATTACTA
*
395175 AATTAATATCTTAAAACTCACTCAAAAAATAACCTTAAATTAATG-TTTCCACAGTGAAAAAAGT
66 AATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGT
395239 ATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTAT-TAAA
131 ATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAA
*
395303 CGCTACCTATTACATTATATAAGCGCTACCTATTACATCAT-TTTTTACCTATTATATTGAAAGT
196 CGATACCTATTAC--TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGT
395367 GTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTT
259 GTCCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTT
395432 TTTTTAATAGTGTTTCATGTTTTCCA-CTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
324 TTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAA
395496 TTA--T--TTGTTTTGATATTTTATAAAATAATATTTAGAA
389 TTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
395533 TTTTTAATTTAATAATAATATATATCGTAACGTGAAAAATAAATCATTAGACGCCTATAATTACT
1 TTTTTAATTTAATAAT-ATATATATCGTAACGTGAAAAATAAATCATTAGACGCCTATAATTACT
* *
395598 AAATTAATATCTTAAAACTCACTCAAAAGATAATCTTAAATTAATGTTTTCCATAGTGAAAAAAG
65 AAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAG
395663 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
130 TATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAA
*
395728 ACGATACATATTACATTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
195 ACGATACCTATTAC--TATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAG
395793 TGTCCATACTTTTT-TACAAAAGGATCGATACTTC-TTTAAAGTTATGTAATTTATGTTTCAATT
258 TGTCCATACTTTTTATA-AAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATT
*
395856 TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACACAAAA
322 TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAA
395921 AATTATTTGATAT-TTTTGATATTTTATAAAATAATATTTAGAA
387 AATTATTTGAT-TGTTTTGATATTTTATAAAATAATATTTAGAA
* *
395964 -TTTAAATTTAACAATAT
1 TTTTTAATTTAATAATAT
395981 TAACCAAAGA
Statistics
Matches: 1234, Mismatches: 23, Indels: 59
0.94 0.02 0.04
Matches are distributed among these distances:
417 62 0.05
418 156 0.13
419 96 0.08
420 23 0.02
421 88 0.07
422 28 0.02
423 45 0.04
424 149 0.12
425 197 0.16
426 174 0.14
427 132 0.11
428 36 0.03
429 3 0.00
430 13 0.01
431 31 0.03
432 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (429 bp):
TTTTTAATTTAATAATATATATATCGTAACGTGAAAAATAAATCATTAGACGCCTATAATTACTA
AATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGT
ATAGACACTTTTATAAAAAGGATAGATACTTTACAATATAAGCACTACCTATTACATTATATAAA
CGATACCTATTACTATATAAGCGCTACCTATTACATCATATTTTTACCTATTATATTGAAAGTGT
CCATACTTTTTATAAAAAGGATCGATACTTCTTTTAAAGTTATGTAATTTATGTTTCAATTTTTT
TTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA
Found at i:394891 original size:23 final size:23
Alignment explanation
Indices: 394865--394927 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
394855 CAATAACCAC
394865 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
394888 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
394911 TACCTATTACATCATAT
1 TACCTATTACATTATAT
394928 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:395333 original size:23 final size:23
Alignment explanation
Indices: 395274--395340 Score: 109
Period size: 22 Copynumber: 3.0 Consensus size: 23
395264 ATACTTTACA
*
395274 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
395297 AT-TAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
395319 ATATAAGCGCTACCTATTACAT
1 ATATAAGCGCTACCTATTACAT
395341 CATTTTTTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.50
23 20 0.50
ACGTcount: A:0.37, C:0.22, G:0.06, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:395739 original size:23 final size:23
Alignment explanation
Indices: 395713--395771 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
395703 AAGCACTACC
395713 TATTACATTATATAAACGATACA
1 TATTACATTATATAAACGATACA
* * *
395736 TATTACATTATATAAGCGCTACC
1 TATTACATTATATAAACGATACA
*
395759 TATTACATCATAT
1 TATTACATTATAT
395772 TTTTACCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (23 bp):
TATTACATTATATAAACGATACA
Found at i:396175 original size:24 final size:24
Alignment explanation
Indices: 396117--396181 Score: 112
Period size: 25 Copynumber: 2.7 Consensus size: 24
396107 CACTCAAAAG
*
396117 ATGTATATACCTAAATATGTAGTT
1 ATGTACATACCTAAATATGTAGTT
396141 ATTGTACATACCTAAATATGTAGTT
1 A-TGTACATACCTAAATATGTAGTT
396166 ATGTACATACCTAAAT
1 ATGTACATACCTAAAT
396182 TTAATGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 16 0.41
25 23 0.59
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.38
Consensus pattern (24 bp):
ATGTACATACCTAAATATGTAGTT
Found at i:398997 original size:385 final size:391
Alignment explanation
Indices: 398286--399979 Score: 2630
Period size: 385 Copynumber: 4.4 Consensus size: 391
398276 TTTAAATTAG
*
398286 TATCGACACAAACTAAAAAAGTGTCGACACGTTATTTAGACATATTCTCTCATAAAA-CGGTATA
1 TATCGACACAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
398350 CTTGTACCGGTTAGATTGAAAAACTACATA-TACATTATACTTTTGGTTTTCGATGTTTTTGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTGGGAT
398414 CGACACTTTGTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGACC-
130 CGACACTTTG--TATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGACCA
* * *
398478 AAACTATCGACACAAACTAAAAAGTGCCGACAC-TTATTTAGACATATTCTCTCATAAAATCGGT
193 AAAATATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGT
*
398542 ATACTTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGTTTTCGA---TTTT-G
258 ATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGTTTTCGATGTTTTTGG
398603 GATCGACACTTTTTATATATGGATC-A-ACTTTATGGTTGCACCCTGTTTCCATTCATTCTGGAC
323 GATCGACAC-TTTTATATATGGATCGACAC-TTATGGTTGCACCCTGTTTCCATTCATTCTGGAC
*
398666 CAAAAA
386 CAAAAC
398672 TATCGACAC-AACTAAAACAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
398736 CTTGTACCGG-TAGATTGAAAAATTACATATTACATTATACTTTTGG-TTTCGATGTTTTGGGAT
65 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTGGGAT
* *
398799 CGACGCTTTGTATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAA
130 CGACACTTTGTATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGACCAAA
*
398864 ACTA-CGACACAAACTAAAAAGTGTCGACACATT-TTTAGACATATTCTCTCAT-AAACCGGTAT
195 AATATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
398926 ACTTGTACCGGTTAGATTGAAAAA-TACATATTACATTATACTTTGGTTTTCGATGTTTTTGGGA
260 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGTTTTCGATGTTTTTGGGA
* *
398990 TCGACACTTTT-TATATGGATCGACACTTATGGTTGCACCCTGTTT---TCCATTCT-GAACAAA
325 TCGACACTTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTCCATTCATTCTGGACCAAA
399050 AC
390 AC
399052 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGAC-TATTCTCTCAT-AAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
399115 TTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGAT
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATG-TTTTGGGAT
*
399179 CGACACTTTTTATATATGGATCGACACTTTA-GGTTGCACCCTATTTTCCATTCATTCTGGACCA
130 CGACAC--TTTGTATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGACCA
*
399243 AAAATATCGACACAGACTAAAACAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
193 AAAATATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGG
*
399308 TATACTTGTACCGGTTAGATTGAAAAA-T---TATTACATTATACTTTGGTTTTTGATGTTTTTG
257 TATACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGTTTTCGATGTTTTTG
* * * *
399369 GGATCGACAC-TTTGTATATGGATCGACACTTATGGTTGCACCTTTTTTCCATTCATTTTGGACC
322 GGATCGACACTTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTCCATTCATTCTGGACC
399433 AAAAC
387 AAAAC
399438 TATCGACACAAACTAAAAAGTGTCGACACA-TATTTAGACATATTCTCTCATAAAACCGG--TAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
399500 TTGTACCGGTTAGATTGAAAAATT--ATATTACATTAT-CTTTTGGTTTTCGATGTTTTTGGGAT
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATG-TTTTGGGAT
* * *
399562 TGACACTTTTTATAT-GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC-AA
130 CGACACTTTGTATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGACCAAA
* *
399625 AA-ATCGACAC-AA--AAACAGTGTCAAC-CATTATTTAGAC--ATT-TCTCATAAAACC-GTAT
195 AATATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTAT
*
399681 ACTTGTATCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGTTTTCGATGTTTTTGGGA
260 ACTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGTTTTCGATGTTTTTGGGA
*
399746 TCGACACTTGTATATA--GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
325 TCGACACTTTTATATATGGATCGACAC-TTATGGTTGCACCCTG-TTTCCATTCATTCTGGACCA
399809 AAAC
388 AAAC
* *
399813 TATCGACACAAACTAAAAAATTTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
399876 TTGTACCGGTTAGATTG-AAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTGGGATC
*
399940 GACACTTTTTATATGGATCGACACTTTATGGTTGCACCCT
131 GACACTTTGTATATGGATCGACACTTTATGGTTGCACCCT
399980 TAATTGGTAT
Statistics
Matches: 1226, Mismatches: 38, Indels: 96
0.90 0.03 0.07
Matches are distributed among these distances:
370 27 0.02
371 13 0.01
372 3 0.00
373 12 0.01
374 97 0.08
375 66 0.05
376 23 0.02
377 35 0.03
378 91 0.07
379 34 0.03
380 69 0.06
381 123 0.10
382 142 0.12
383 150 0.12
384 71 0.06
385 166 0.14
386 97 0.08
387 7 0.01
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (391 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTGGGATC
GACACTTTGTATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGACCAAAA
ATATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTGGTTTTCGATGTTTTTGGGAT
CGACACTTTTATATATGGATCGACACTTATGGTTGCACCCTGTTTCCATTCATTCTGGACCAAAA
C
Found at i:399009 original size:192 final size:196
Alignment explanation
Indices: 398286--399979 Score: 2629
Period size: 191 Copynumber: 8.9 Consensus size: 196
398276 TTTAAATTAG
*
398286 TATCGACACAAACTAAAAAAGTGTCGACACGTTATTTAGACATATTCTCTCATAAAA-CGGTATA
1 TATCGACACAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
398350 CTTGTACCGGTTAGATTGAAAAACTACATA-TACATTATACTTTTGGTTTTCGATGTTTTT-GGA
65 CTTGTACCGGTTAGATTGAAAAA-TACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
398413 TCGACACTTTGTATATATGGATCGACACTTTATGGTTGCACCCTATTTTCCATTCATTCTGGACC
129 TCGACACTTT-T-TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
398478 -AAAC
192 AAAAC
* *
398482 TATCGACACAAACTAAAAAGTGCCGACAC-TTATTTAGACATATTCTCTCATAAAATCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
398546 TTGTATCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGTTTTCGA---TTTT-GGAT
66 TTGTACCGGTTAGATTGAAAAA-TACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGAT
398606 CGACACTTTTTATATATGGATC-A-ACTTTATGGTTGCACCCTG-TTTCCATTCATTCTGGACCA
130 CGACAC-TTTT-TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCA
*
398668 AAAA
193 AAAC
398672 TATCGACAC-AACTAAAACAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
398736 CTTGTACCGG-TAGATTGAAAAATTACATATTACATTATACTTTTGG-TTTCGATG-TTTTGGGA
65 CTTGTACCGGTTAGATTGAAAAA-TACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
398798 TCGACGCTTTGTATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
129 TCGACACTTTTTATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
398863 AAC
194 AAC
398866 TA-CGACACAAACTAAAAAGTGTCGACACATT-TTTAGACATATTCTCTCAT-AAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
398928 TTGTACCGGTTAGATTGAAAAATACATATTACATTATAC-TTTGGTTTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
*
398992 GACACTTTTTATATGGATCGACAC-TTATGGTTGCACCCTGTTTT-C---CATTCT-GAACAAAA
131 GACACTTTTTATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAA
399051 C
196 C
399052 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGAC-TATTCTCTCAT-AAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
399115 TTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
*
399180 GACACTTTTTATATATGGATCGACACTTTA-GGTTGCACCCTATTTTCCATTCATTCTGGACCAA
131 GACAC-TTTT-TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAA
*
399244 AAA
194 AAC
*
399247 TATCGACACAGACTAAAACAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAA-AGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
399312 CTTGTACCGGTTAGATTGAAAAAT---TATTACATTATAC-TTTGGTTTTTGATGTTTTTGGGAT
65 CTTGTACCGGTTAGATTGAAAAATACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGAT
* * *
399373 CGACACTTTGTATATGGATCGACAC-TTATGGTTGCA-CCTTTTTTCCATTCATTTTGGACCAAA
130 CGACACTTTTTATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAA
399436 AC
195 AC
399438 TATCGACACAAACTAAAAAGTGTCGACACA-TATTTAGACATATTCTCTCATAAAACCGG--TAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
* *
399500 TTGTACCGGTTAGATTGAAAAAT-TATATTACATTAT-CTTTTGGTTTTCGATGTTTTTGGGATT
66 TTGTACCGGTTAGATTGAAAAATACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
399563 GACACTTTTTATAT-GATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAA
131 GACACTTTTTATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAA
399627 -
196 C
* *
399627 -ATCGACAC-AA--AAACAGTGTCAAC-CATTATTTAGAC--ATT-TCTCATAAAACC-GTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
399683 TTGTATCGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGTTTTCGATGTTTTTGGGAT
66 TTGTACCGGTTAGATTGAAAAA-TACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGAT
* *
399747 CGACAC-TTGTATATAGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAA
130 CGACACTTTTTATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAA
399811 AC
195 AC
* *
399813 TATCGACACAAACTAAAAAATTTCG--ACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
1 TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
*
399876 TTGTACCGGTTAGATTGAAAATTACATATTACATTATACTTTTGGTTTTCGATG-TTTTGGGATC
66 TTGTACCGGTTAGATTGAAAAATACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
399940 GACACTTTTTATATGGATCGACACTTTATGGTTGCACCCT
131 GACACTTTTTATATGGATCGACACTTTATGGTTGCACCCT
399980 TAATTGGTAT
Statistics
Matches: 1397, Mismatches: 45, Indels: 115
0.90 0.03 0.07
Matches are distributed among these distances:
181 1 0.00
182 12 0.01
183 27 0.02
184 10 0.01
185 111 0.08
186 11 0.01
187 132 0.09
188 57 0.04
189 130 0.09
190 157 0.11
191 177 0.13
192 163 0.12
193 126 0.09
194 94 0.07
195 98 0.07
196 46 0.03
197 11 0.01
198 34 0.02
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.36
Consensus pattern (196 bp):
TATCGACACAAACTAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATAC
TTGTACCGGTTAGATTGAAAAATACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGATC
GACACTTTTTATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACCAAAA
C
Found at i:400082 original size:17 final size:17
Alignment explanation
Indices: 400060--400101 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
400050 TCTCTTTCAT
*
400060 AATTATATTCACATACA
1 AATTATAATCACATACA
**
400077 AATTATAATCGTATACA
1 AATTATAATCACATACA
400094 AATTATAA
1 AATTATAA
400102 ATCTTATACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.50, C:0.12, G:0.02, T:0.36
Consensus pattern (17 bp):
AATTATAATCACATACA
Found at i:400109 original size:18 final size:17
Alignment explanation
Indices: 400072--400113 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
400062 TTATATTCAC
400072 ATACAAATTATAATCGT
1 ATACAAATTATAATCGT
*
400089 ATACAAATTATAAATCTT
1 ATACAAATTAT-AATCGT
400107 ATACAAA
1 ATACAAA
400114 ATTAACCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.33
Consensus pattern (17 bp):
ATACAAATTATAATCGT
Found at i:401680 original size:16 final size:16
Alignment explanation
Indices: 401661--401708 Score: 51
Period size: 18 Copynumber: 2.9 Consensus size: 16
401651 TCCTCCTCTC
401661 TTTTCTTCTTCATATT
1 TTTTCTTCTTCATATT
*
401677 TTTTCAGTTCATCATATT
1 TTTTC--TTCTTCATATT
* *
401695 TTTTTTTCTACATA
1 TTTTCTTCTTCATA
401709 GCTCTTCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
16 12 0.46
18 14 0.54
ACGTcount: A:0.19, C:0.17, G:0.02, T:0.62
Consensus pattern (16 bp):
TTTTCTTCTTCATATT
Found at i:401986 original size:21 final size:21
Alignment explanation
Indices: 401937--401997 Score: 88
Period size: 21 Copynumber: 3.0 Consensus size: 21
401927 CCCCTATGCC
* * *
401937 TCAAGTGTATCTTCGACTCTC
1 TCAAGTTTCTCTTCGACTCTA
401958 TC-AGTTTCTCTTCGACTCTA
1 TCAAGTTTCTCTTCGACTCTA
401978 TCAAGTTTCTCTTCGACTCT
1 TCAAGTTTCTCTTCGACTCT
401998 TGATTGTCTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.16, C:0.30, G:0.11, T:0.43
Consensus pattern (21 bp):
TCAAGTTTCTCTTCGACTCTA
Found at i:404382 original size:172 final size:172
Alignment explanation
Indices: 404094--404520 Score: 509
Period size: 172 Copynumber: 2.5 Consensus size: 172
404084 CGTACTTACG
* *
404094 AAAGTATCG--ACTTTCAATATAT-CGGTATCATTTTA-CGGTTTTATCATTTTGATACCGG-TT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTT-ATACCGGTTT
** **
404154 TATCATATTTTACCTGTTATATCGTTGTGGATCGATATTTTTTTTAAGTATCGACACATTATAGG
65 TATCATATTTTA-CTG-T-TATCGTACTGGATCGATATTTTTTAAAAGTATCGACAC--TATAGG
404219 -CGTAAAAC-GCTTCTCTTTAAATTCACAAAGTGTCGATCCTTATA-T
125 ACGTAAAACTGCTTCTCTTTAAATTCACAAAGTGTCGATCCTTATATT
*
404264 AAAGTATCGACACGTTCAATATATCCGGTAAACGTTTTACCGGTTTTATCATTTTATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGT-AACGTTTTACCGGTTTTATCATTTTATACCGGTTT
**
404329 TATCATATTTTACTG-TATC-TACTGGATCGATACATTTTTTAAAAGTATCGACACTATAGGATT
65 TATCATATTTTACTGTTATCGTACTGGATCGAT--ATTTTTTAAAAGTATCGACACTATAGGACG
*
404392 TAAAACTGCTTCTCTTTAAATTCACGAAGTGTCGATCCTTATATT
128 TAAAACTGCTTCTCTTTAAATTCACAAAGTGTCGATCCTTATATT
* * * * * *
404437 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACC-GATTTATCATTTTTATACC-GTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCA-TTTTATACCGGTTT
*
404500 TGTCATAGTTTTACCTGTTAT
65 TATCATA-TTTTA-CTGTTAT
404521 ATCGTTTTGG
Statistics
Matches: 224, Mismatches: 18, Indels: 26
0.84 0.07 0.10
Matches are distributed among these distances:
170 25 0.11
171 28 0.12
172 89 0.40
173 33 0.15
174 20 0.09
175 29 0.13
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (172 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTATACCGGTTTT
ATCATATTTTACTGTTATCGTACTGGATCGATATTTTTTAAAAGTATCGACACTATAGGACGTAA
AACTGCTTCTCTTTAAATTCACAAAGTGTCGATCCTTATATT
Found at i:407213 original size:41 final size:42
Alignment explanation
Indices: 407114--407233 Score: 197
Period size: 41 Copynumber: 2.9 Consensus size: 42
407104 TTTTCCCGAA
**
407114 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAAATATTT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGG-AAATACGT
*
407157 TTCCCGTGTTTGTTTCACGTAATTCATTTTCCGGAAA-ACGT
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAATACGT
407198 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
1 TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAA
407234 TGTAATTCAT
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
41 37 0.51
42 3 0.04
43 33 0.45
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.44
Consensus pattern (42 bp):
TTCCCGTGTTTGTTTCACGTAATTCGTTTTCCGGAAATACGT
Found at i:407455 original size:16 final size:16
Alignment explanation
Indices: 407434--407497 Score: 55
Period size: 16 Copynumber: 4.2 Consensus size: 16
407424 ATATATTTAT
407434 TAATATTATAATAATA
1 TAATATTATAATAATA
**
407450 TAATATTATTTTAATA
1 TAATATTATAATAATA
*
407466 T-ATA--AAAATAATCA
1 TAATATTATAATAAT-A
*
407480 -ATTATTATAATAATA
1 TAATATTATAATAATA
407495 TAA
1 TAA
407498 GATATTATAT
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
13 5 0.14
14 3 0.09
15 4 0.11
16 23 0.66
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATATTATAATAATA
Found at i:407455 original size:26 final size:26
Alignment explanation
Indices: 407426--407496 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 26
407416 TATTTAAAAT
*
407426 ATATT-TATTAATATTATAATAATATA
1 ATATTATATTAATA-TATAAAAATATA
*
407452 ATATTATTTTAATATATAAAAATAATCA
1 ATATTATATTAATATATAAAAAT-AT-A
*
407480 ATTATTATAATAATATA
1 A-TATTATATTAATATA
407497 AGATATTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 13 0.35
27 9 0.24
28 2 0.05
29 13 0.35
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (26 bp):
ATATTATATTAATATATAAAAATATA
Found at i:407458 original size:48 final size:45
Alignment explanation
Indices: 407406--407497 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
407396 CAAAATATTA
* *
407406 ATTATTAAAATATTTAAAATATATTTATTAA-TATTATAATAATATAAT
1 ATTATTAAAATATATAAAA-ATA---ATCAATTATTATAATAATATAAT
**
407454 ATTATTTTAATATATAAAAATAATCAATTATTATAATAATATAA
1 ATTATTAAAATATATAAAAATAATCAATTATTATAATAATATAA
407498 GATATTATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
44 4 0.10
45 16 0.41
47 3 0.08
48 16 0.41
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (45 bp):
ATTATTAAAATATATAAAAATAATCAATTATTATAATAATATAAT
Found at i:407825 original size:20 final size:20
Alignment explanation
Indices: 407747--407816 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
407737 TTTCCAGATG
407747 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
407767 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
* *
407787 TTTTACATAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
407807 TTTTCCAGAA
1 TTTTCCAGAA
407817 TTCAAATTCC
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:407835 original size:15 final size:15
Alignment explanation
Indices: 407799--407865 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
407789 TTACATAAAT
**
407799 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
407814 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
407828 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
407843 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
407858 GTAATTCA
1 GTAATTCA
407866 TTTTCTAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.27
15 33 0.73
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:407841 original size:29 final size:30
Alignment explanation
Indices: 407799--407870 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
407789 TTACATAAAT
407799 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
407828 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
407858 GTAATTCATTTTC
1 GTAATTCATTTTC
407871 TAAAAAACCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:412113 original size:22 final size:22
Alignment explanation
Indices: 412088--412139 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
412078 AACTAGTACT
412088 AAAGTGC-CTCGACACTGACACA
1 AAAGTGCACTC-ACACTGACACA
* *
412110 AAAGTGCATTCACACTGATACA
1 AAAGTGCACTCACACTGACACA
412132 AAAGTGCA
1 AAAGTGCA
412140 TTCGCATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 25 0.93
23 2 0.07
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAGTGCACTCACACTGACACA
Found at i:412140 original size:22 final size:22
Alignment explanation
Indices: 412099--412158 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
412089 AAGTGCCTCG
*
412099 ACACTGACACAAAAGTGCATTC
1 ACACTGATACAAAAGTGCATTC
412121 ACACTGATACAAAAGTGCATTC
1 ACACTGATACAAAAGTGCATTC
* * *
412143 GCATTGATACTAAAGT
1 ACACTGATACAAAAGT
412159 ACCTTAGCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (22 bp):
ACACTGATACAAAAGTGCATTC
Found at i:413540 original size:2 final size:2
Alignment explanation
Indices: 413533--413568 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
413523 AAAGTTTTGA
413533 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
413569 GTATTTATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:418685 original size:21 final size:21
Alignment explanation
Indices: 418659--418698 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
418649 CAGAACCCCA
*
418659 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
418680 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
418699 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:429108 original size:2 final size:2
Alignment explanation
Indices: 429055--429088 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
429045 TGTACAATAC
429055 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
429089 TTCTATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:430862 original size:30 final size:29
Alignment explanation
Indices: 430820--430891 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 29
430810 ATATTTTTAG
*
430820 TTATTAGAATTTT-AAAAATTATAAAATAC
1 TTATTA-AATTTTCAAAAATTATAAAATAA
**
430849 TTATTTAATATTTTCAATTATTATAAAATAA
1 TTA-TTAA-ATTTTCAAAAATTATAAAATAA
430880 TTATTAAATTTT
1 TTATTAAATTTT
430892 GTCAAACTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
29 9 0.24
30 12 0.32
31 16 0.43
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (29 bp):
TTATTAAATTTTCAAAAATTATAAAATAA
Found at i:430873 original size:31 final size:32
Alignment explanation
Indices: 430837--430911 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
430827 AATTTTAAAA
* * *
430837 ATTATAAAATACTTATTTAATATTT-TC-AATT
1 ATTATAAAATAATTATTAAAT-TTTGTCAAACT
430868 ATTATAAAATAATTATTAAATTTTGTCAAACT
1 ATTATAAAATAATTATTAAATTTTGTCAAACT
*
430900 ATTACAAAATAA
1 ATTATAAAATAA
430912 ATCTTGAGCA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 3 0.08
31 21 0.55
32 14 0.37
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (32 bp):
ATTATAAAATAATTATTAAATTTTGTCAAACT
Found at i:437480 original size:29 final size:29
Alignment explanation
Indices: 437438--437498 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
437428 AGTAGTCTTA
437438 CAAGTCGCCATGTAATCAAAACGACCAAG
1 CAAGTCGCCATGTAATCAAAACGACCAAG
*
437467 CAAGTCGTCATGTAATCAAAACGACCAAG
1 CAAGTCGCCATGTAATCAAAACGACCAAG
437496 CAA
1 CAA
437499 AGGTAGCCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.43, C:0.26, G:0.16, T:0.15
Consensus pattern (29 bp):
CAAGTCGCCATGTAATCAAAACGACCAAG
Found at i:438114 original size:38 final size:38
Alignment explanation
Indices: 438007--438110 Score: 99
Period size: 37 Copynumber: 2.8 Consensus size: 38
437997 TTTGTTGAAT
* * *
438007 TTATATTATATTAAAAATTTAGTTAATTA---ATTTAAG
1 TTATATTATAATAAAAA-ATAGTTTATTAGTTATTTAAG
* *
438043 TTATGTTATAATAAAAAATAGTTTATTAGTTATTTCAG
1 TTATATTATAATAAAAAATAGTTTATTAGTTATTTAAG
* * *
438081 TTATATTTTAA-AAAAATTAGTTTGTTAGTT
1 TTATATTATAATAAAAAATAGTTTATTAGTT
438111 TATTAGTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
35 9 0.16
36 15 0.27
37 17 0.30
38 15 0.27
ACGTcount: A:0.40, C:0.01, G:0.09, T:0.50
Consensus pattern (38 bp):
TTATATTATAATAAAAAATAGTTTATTAGTTATTTAAG
Found at i:438161 original size:14 final size:14
Alignment explanation
Indices: 438117--438154 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
438107 AGTTTATTAG
438117 TTTAGGATTTAGGGT
1 TTTAGG-TTTAGGGT
438132 TTATA-GTTTAGGGT
1 TT-TAGGTTTAGGGT
438146 TTTAGGTTT
1 TTTAGGTTT
438155 TAGGTTTCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 2 0.10
14 14 0.67
15 3 0.14
16 2 0.10
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (14 bp):
TTTAGGTTTAGGGT
Found at i:438313 original size:36 final size:37
Alignment explanation
Indices: 438262--438341 Score: 110
Period size: 39 Copynumber: 2.1 Consensus size: 37
438252 TTGTTGAATA
438262 TATATTATATAAAAA-A-TTTAGTTAATTAGTTTAAGT
1 TATATTATATAAAAATAGTTTA-TTAATTAGTTTAAGT
*
438298 TATATTATAATAAAAAATAGTTTATTAGTTAGTTTAAGT
1 TATATTAT-AT-AAAAATAGTTTATTAATTAGTTTAAGT
438337 TATAT
1 TATAT
438342 AAAAGAATAG
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
36 8 0.21
37 2 0.05
38 5 0.13
39 20 0.51
40 4 0.10
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (37 bp):
TATATTATATAAAAATAGTTTATTAATTAGTTTAAGT
Found at i:438343 original size:36 final size:37
Alignment explanation
Indices: 438260--438368 Score: 104
Period size: 39 Copynumber: 3.0 Consensus size: 37
438250 GTTTGTTGAA
*
438260 TATATATTATATAAAAA-A-TTTAGTTAATTAGTTTAAGT
1 TATATA-TATA-AAAAATAGTTTA-TTAGTTAGTTTAAGT
438298 TATATTATAATAAAAAATAGTTTATTAGTTAGTTTAAG-
1 TATA-TAT-ATAAAAAATAGTTTATTAGTTAGTTTAAGT
* *
438336 T-TATATA-AAAGAATAGTGTATTAGTT-GTTTAAG
1 TATATATATAAAAAATAGTTTATTAGTTAGTTTAAG
438369 GGGAAAATTC
Statistics
Matches: 64, Mismatches: 3, Indels: 13
0.80 0.04 0.16
Matches are distributed among these distances:
33 7 0.11
34 17 0.27
35 1 0.02
36 3 0.05
37 2 0.03
38 11 0.17
39 19 0.30
40 4 0.06
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (37 bp):
TATATATATAAAAAATAGTTTATTAGTTAGTTTAAGT
Found at i:438366 original size:33 final size:34
Alignment explanation
Indices: 438302--438368 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
438292 TTAAGTTATA
*
438302 TTATAATAAAAAATAGTTTATTAGTTAGTTTAAG
1 TTATAATAAAAAATAGTGTATTAGTTAGTTTAAG
438336 TTAT-ATAAAAGAATAGTGTATTAGTT-GTTTAAG
1 TTATAATAAAA-AATAGTGTATTAGTTAGTTTAAG
438369 GGGAAAATTC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 13 0.42
34 18 0.58
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.43
Consensus pattern (34 bp):
TTATAATAAAAAATAGTGTATTAGTTAGTTTAAG
Found at i:438420 original size:22 final size:21
Alignment explanation
Indices: 438394--438499 Score: 85
Period size: 22 Copynumber: 5.0 Consensus size: 21
438384 TAAGTTATGA
438394 TTTAGGGTTTATAGTTT-GTTAG
1 TTTAGGGTTTATAGTTTAG-T-G
*
438416 TTTAGGGTTTATAATTTAGTG
1 TTTAGGGTTTATAGTTTAGTG
438437 TTTAGGGTTTTATAGTTTA-TG
1 TTTAGGG-TTTATAGTTTAGTG
* * *
438458 ATTTAGTGTTTGGT-GATTAGTG
1 -TTTAGGGTTT-ATAGTTTAGTG
*
438480 TTTAGTGTTTAGT-GTTTAGT
1 TTTAGGGTTTA-TAGTTTAGT
438500 AATTAGTGTT
Statistics
Matches: 71, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
21 34 0.48
22 36 0.51
23 1 0.01
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (21 bp):
TTTAGGGTTTATAGTTTAGTG
Found at i:438439 original size:14 final size:15
Alignment explanation
Indices: 438416--438518 Score: 94
Period size: 14 Copynumber: 7.3 Consensus size: 15
438406 AGTTTGTTAG
* *
438416 TTTAGGGTTTA-TAA
1 TTTAGTGTTTAGTGA
* *
438430 TTTAGTGTTTAGGGT
1 TTTAGTGTTTAGTGA
438445 TTTA-TAGTTTA-TGA
1 TTTAGT-GTTTAGTGA
*
438459 TTTAGTGTTTGGTGA
1 TTTAGTGTTTAGTGA
438474 -TTAGTGTTTAGTG-
1 TTTAGTGTTTAGTGA
438487 TTTAGTGTTTAGT-A
1 TTTAGTGTTTAGTGA
*
438501 ATTAGTGTTTAGTG-
1 TTTAGTGTTTAGTGA
438515 TTTA
1 TTTA
438519 TGATTTAAGG
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
14 59 0.82
15 13 0.18
ACGTcount: A:0.20, C:0.00, G:0.25, T:0.54
Consensus pattern (15 bp):
TTTAGTGTTTAGTGA
Found at i:438486 original size:7 final size:7
Alignment explanation
Indices: 438430--438518 Score: 92
Period size: 7 Copynumber: 12.6 Consensus size: 7
438420 GGGTTTATAA
438430 TTTAGTG
1 TTTAGTG
*
438437 TTTAGGG
1 TTTAGTG
438444 TTTTA-TAG
1 -TTTAGT-G
438452 TTTA-TG
1 TTTAGTG
438458 ATTTAGTG
1 -TTTAGTG
*
438466 TTTGGTG
1 TTTAGTG
*
438473 ATTAGTG
1 TTTAGTG
438480 TTTAGTG
1 TTTAGTG
438487 TTTAGTG
1 TTTAGTG
*
438494 TTTAGTA
1 TTTAGTG
*
438501 ATTAGTG
1 TTTAGTG
438508 TTTAGTG
1 TTTAGTG
438515 TTTA
1 TTTA
438519 TGATTTAAGG
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
6 1 0.01
7 60 0.88
8 7 0.10
ACGTcount: A:0.19, C:0.00, G:0.26, T:0.55
Consensus pattern (7 bp):
TTTAGTG
Found at i:438575 original size:7 final size:7
Alignment explanation
Indices: 438560--438710 Score: 63
Period size: 7 Copynumber: 21.7 Consensus size: 7
438550 GCATATACTA
438560 TAAACCC
1 TAAACCC
*
438567 TAAATCC
1 TAAACCC
*
438574 TAAACTC
1 TAAACCC
*
438581 T-AACCT
1 TAAACCC
* *
438587 TAAATCA
1 TAAACCC
**
438594 TAAACTA
1 TAAACCC
438601 TAAA-CC
1 TAAACCC
* *
438607 TTAGCCC
1 TAAACCC
*
438614 TTAAACTC
1 -TAAACCC
438622 TAAACCC
1 TAAACCC
438629 TAAACCC
1 TAAACCC
*
438636 TAAACCA
1 TAAACCC
* **
438643 AAAACTA
1 TAAACCC
438650 TAAACCC
1 TAAACCC
**
438657 TAAACAA
1 TAAACCC
* *
438664 TAAATCT
1 TAAACCC
**
438671 TAAATAC
1 TAAACCC
* *
438678 TAGACCT
1 TAAACCC
* *
438685 TAGACTC
1 TAAACCC
438692 TAAACCC
1 TAAACCC
438699 TAAACCC
1 TAAACCC
438706 TAAAC
1 TAAAC
438711 TATAGTTTAG
Statistics
Matches: 103, Mismatches: 38, Indels: 6
0.70 0.26 0.04
Matches are distributed among these distances:
6 6 0.06
7 93 0.90
8 4 0.04
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:438632 original size:14 final size:14
Alignment explanation
Indices: 438560--438710 Score: 76
Period size: 14 Copynumber: 10.9 Consensus size: 14
438550 GCATATACTA
* *
438560 TAAACCCTAAATCC
1 TAAACTCTAAACCC
*
438574 TAAACTCT-AACCT
1 TAAACTCTAAACCC
**
438587 TAAA-TCATAAACTA
1 TAAACTC-TAAACCC
* *
438601 TAAAC-CTTAGCCC
1 TAAACTCTAAACCC
438614 TTAAACTCTAAACCC
1 -TAAACTCTAAACCC
* *
438629 TAAACCCTAAACCA
1 TAAACTCTAAACCC
* *
438643 AAAACTATAAACCC
1 TAAACTCTAAACCC
** * *
438657 TAAACAATAAATCT
1 TAAACTCTAAACCC
* *
438671 TAAA-TACTAGACCT
1 TAAACT-CTAAACCC
*
438685 TAGACTCTAAACCC
1 TAAACTCTAAACCC
*
438699 TAAACCCTAAAC
1 TAAACTCTAAAC
438711 TATAGTTTAG
Statistics
Matches: 100, Mismatches: 30, Indels: 14
0.69 0.21 0.10
Matches are distributed among these distances:
12 2 0.02
13 11 0.11
14 80 0.80
15 7 0.07
ACGTcount: A:0.46, C:0.29, G:0.02, T:0.23
Consensus pattern (14 bp):
TAAACTCTAAACCC
Found at i:438639 original size:21 final size:21
Alignment explanation
Indices: 438560--438640 Score: 76
Period size: 20 Copynumber: 3.9 Consensus size: 21
438550 GCATATACTA
*
438560 TAAACCCTAAATCCTAAACTC
1 TAAACCCTAAACCCTAAACTC
* * * *
438581 T-AACCTTAAATCATAAACTA
1 TAAACCCTAAACCCTAAACTC
* *
438601 TAAA-CCTTAGCCCTTAAACTC
1 TAAACCCTAAACCC-TAAACTC
438622 TAAACCCTAAACCCTAAAC
1 TAAACCCTAAACCCTAAAC
438641 CAAAAACTAT
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
20 21 0.46
21 18 0.39
22 7 0.15
ACGTcount: A:0.43, C:0.31, G:0.01, T:0.25
Consensus pattern (21 bp):
TAAACCCTAAACCCTAAACTC
Found at i:438761 original size:7 final size:7
Alignment explanation
Indices: 438751--438782 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
438741 AGGTTTAGTG
*
438751 TTTATGA
1 TTTAAGA
438758 TTTAAGA
1 TTTAAGA
438765 TTTAAGA
1 TTTAAGA
438772 TTTAAGA
1 TTTAAGA
438779 TTTA
1 TTTA
438783 TTGTTTAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (7 bp):
TTTAAGA
Found at i:438763 original size:21 final size:22
Alignment explanation
Indices: 438728--438768 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
438718 TAGTTTGTTA
* *
438728 GTTTATTAGTTTAAGGTTTAGT
1 GTTTATGAGTTTAAGATTTAGT
438750 GTTTATGA-TTTAAGATTTA
1 GTTTATGAGTTTAAGATTTA
438769 AGATTTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.54
Consensus pattern (22 bp):
GTTTATGAGTTTAAGATTTAGT
Found at i:438834 original size:7 final size:7
Alignment explanation
Indices: 438818--438884 Score: 53
Period size: 7 Copynumber: 9.6 Consensus size: 7
438808 ACATGAGTGG
*
438818 AAACCTT
1 AAACCCT
438825 AAACCCT
1 AAACCCT
*
438832 AAACACT
1 AAACCCT
***
438839 AAATATT
1 AAACCCT
*
438846 AAATCCT
1 AAACCCT
*
438853 AAACCAT
1 AAACCCT
**
438860 AAACTAT
1 AAACCCT
438867 AAACCCT
1 AAACCCT
438874 AAACCCT
1 AAACCCT
438881 AAAC
1 AAAC
438885 TAACAAACTA
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 49 1.00
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:438853 original size:21 final size:21
Alignment explanation
Indices: 438823--438886 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
438813 AGTGGAAACC
438823 TTAAACCCTAAACACTAAA-TA
1 TTAAACCCTAAAC-CTAAACTA
*
438844 TTAAATCCTAAACCATAAACTA
1 TTAAACCCTAAACC-TAAACTA
438866 -TAAACCCTAAACCCTAAACTA
1 TTAAACCCTAAA-CCTAAACTA
438887 ACAAACTAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
20 1 0.03
21 33 0.87
22 4 0.11
ACGTcount: A:0.50, C:0.27, G:0.00, T:0.23
Consensus pattern (21 bp):
TTAAACCCTAAACCTAAACTA
Found at i:438930 original size:35 final size:36
Alignment explanation
Indices: 438889--438975 Score: 101
Period size: 35 Copynumber: 2.5 Consensus size: 36
438879 CTAAACTAAC
*
438889 AAACTAACAAACTAATTCTTTTA-TATAACT-TAAATT
1 AAACTAATAAACTAATT-TTTTATTATAA-TATAAATT
* *
438925 -AACTAATAAACT-GTTTTTTATTATAATATAACTT
1 AAACTAATAAACTAATTTTTTATTATAATATAAATT
438959 AAACTAATAAACTAATT
1 AAACTAATAAACTAATT
438976 AACTAAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 6 0.14
34 12 0.28
35 23 0.53
36 2 0.05
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.40
Consensus pattern (36 bp):
AAACTAATAAACTAATTTTTTATTATAATATAAATT
Found at i:439117 original size:22 final size:22
Alignment explanation
Indices: 439098--439148 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
439088 AATAAACTCG
*
439098 GAAACTCTAAACCCTAAACTAA
1 GAAACTATAAACCCTAAACTAA
*
439120 TAAACTATAAACCCTAAACTAA
1 GAAACTATAAACCCTAAACTAA
*
439142 CAAACTA
1 GAAACTA
439149 ACAAACTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.53, C:0.25, G:0.02, T:0.20
Consensus pattern (22 bp):
GAAACTATAAACCCTAAACTAA
Found at i:439190 original size:35 final size:35
Alignment explanation
Indices: 439143--439245 Score: 115
Period size: 35 Copynumber: 2.9 Consensus size: 35
439133 CTAAACTAAC
*
439143 AAACTAACAAACTAATTCTTTTATATAACT-TAAAC-T
1 AAACTAATAAACTAATT-TTTTATATAA-TAT-AACTT
439179 -AACTAATAAACT-ATTTTTTATTATAATATAACTT
1 AAACTAATAAACTAATTTTTTA-TATAATATAACTT
*
439213 AAACTAATTAACTAATTTTTTTATATAATATAA
1 AAACTAATAAACTAA-TTTTTTATATAATATAA
439246 ATTCAACAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 12
0.81 0.03 0.16
Matches are distributed among these distances:
33 9 0.15
34 10 0.17
35 22 0.37
36 11 0.19
37 7 0.12
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.43
Consensus pattern (35 bp):
AAACTAATAAACTAATTTTTTATATAATATAACTT
Found at i:439208 original size:39 final size:36
Alignment explanation
Indices: 439165--439245 Score: 110
Period size: 39 Copynumber: 2.2 Consensus size: 36
439155 TAATTCTTTT
439165 ATATAACTTAAACTAACTAA-TAAACTATTTTTTATTATA
1 ATATAACTTAAACTAACTAACT-AA-T-TTTTTTA-TATA
*
439204 ATATAACTTAAACTAATTAACTAATTTTTTTATATA
1 ATATAACTTAAACTAACTAACTAATTTTTTTATATA
439240 ATATAA
1 ATATAA
439246 ATTCAACAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
36 10 0.25
37 7 0.17
38 1 0.03
39 21 0.52
40 1 0.03
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (36 bp):
ATATAACTTAAACTAACTAACTAATTTTTTTATATA
Found at i:439838 original size:20 final size:20
Alignment explanation
Indices: 439813--439855 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
439803 TTTTTCAACG
*
439813 CATTATCTAAAAAATTTTGC
1 CATTATCTAAAAAATTTAGC
439833 CATTATCTAAAAAATTTAGC
1 CATTATCTAAAAAATTTAGC
439853 CAT
1 CAT
439856 CAATAATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.37
Consensus pattern (20 bp):
CATTATCTAAAAAATTTAGC
Found at i:441130 original size:15 final size:15
Alignment explanation
Indices: 441110--441157 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
441100 TTAGCTGGGT
*
441110 GGGCGGATGTGGGGC
1 GGGCGGATGCGGGGC
441125 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
441140 GGGCGGATGCGGGGC
1 GGGCGGATGCGGGGC
441155 GGG
1 GGG
441158 TAATGTCTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.06, C:0.17, G:0.69, T:0.08
Consensus pattern (15 bp):
GGGCGGATGCGGGGC
Found at i:443637 original size:2 final size:2
Alignment explanation
Indices: 443630--443661 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
443620 AACTACAGAA
443630 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
443662 GTATGAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:446042 original size:26 final size:26
Alignment explanation
Indices: 446013--446062 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
446003 TGAGTATCGT
446013 TAAACATCGTTAAACATTATTAATAG
1 TAAACATCGTTAAACATTATTAATAG
* *
446039 TAAAGATCGTTAAATATTATTAAT
1 TAAACATCGTTAAACATTATTAAT
446063 TTAATTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (26 bp):
TAAACATCGTTAAACATTATTAATAG
Found at i:446158 original size:21 final size:21
Alignment explanation
Indices: 446121--446160 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
446111 AATTAATTAA
446121 AAAATTAAATATAAATTATTT
1 AAAATTAAATATAAATTATTT
*
446142 AAAA-TAAATAATTAATTAT
1 AAAATTAAAT-ATAAATTAT
446161 ATTATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
AAAATTAAATATAAATTATTT
Found at i:447117 original size:57 final size:57
Alignment explanation
Indices: 447054--447167 Score: 228
Period size: 57 Copynumber: 2.0 Consensus size: 57
447044 TACGTTCGAC
447054 GAGTATCACTAACGATGAATATTATTAATTTAATTAATAAAATTTTAAAATTAAAAA
1 GAGTATCACTAACGATGAATATTATTAATTTAATTAATAAAATTTTAAAATTAAAAA
447111 GAGTATCACTAACGATGAATATTATTAATTTAATTAATAAAATTTTAAAATTAAAAA
1 GAGTATCACTAACGATGAATATTATTAATTTAATTAATAAAATTTTAAAATTAAAAA
447168 AGACTCGTCG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 57 1.00
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.37
Consensus pattern (57 bp):
GAGTATCACTAACGATGAATATTATTAATTTAATTAATAAAATTTTAAAATTAAAAA
Found at i:447966 original size:2 final size:2
Alignment explanation
Indices: 447959--447986 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
447949 TTACAACTTA
447959 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
447987 CTCAATTGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:450779 original size:22 final size:22
Alignment explanation
Indices: 450751--450825 Score: 89
Period size: 22 Copynumber: 3.4 Consensus size: 22
450741 TTGCAATGCT
450751 AAGGCACTTTAGTATCAGTGCG
1 AAGGCACTTTAGTATCAGTGCG
* *
450773 AATGCACTTTTGTATCAGTGTCG
1 AAGGCACTTTAGTATCAGTG-CG
* * *
450796 -AGGCACTTTAATACCAGTGCT
1 AAGGCACTTTAGTATCAGTGCG
450817 AAGGCACTT
1 AAGGCACTT
450826 CCGTGTATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.02
22 41 0.93
23 2 0.05
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.31
Consensus pattern (22 bp):
AAGGCACTTTAGTATCAGTGCG
Found at i:451821 original size:19 final size:19
Alignment explanation
Indices: 451771--451825 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 19
451761 GCCGTTGCAG
451771 TCAGGGTGTATCGATACAC
1 TCAGGGTGTATCGATACAC
* *
451790 T-A--CTGTATGGATACAC
1 TCAGGGTGTATCGATACAC
451806 TCAGGGTGTATCGATACAC
1 TCAGGGTGTATCGATACAC
451825 T
1 T
451826 ATTTGCATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 13 0.45
17 1 0.03
18 1 0.03
19 14 0.48
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (19 bp):
TCAGGGTGTATCGATACAC
Found at i:451918 original size:20 final size:20
Alignment explanation
Indices: 451893--451943 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 20
451883 GATACACCAT
451893 TGTATGGATACACTGC-AGAG
1 TGTATGGATACACTGCAAG-G
451913 TGTATGGATACACTGCAAGG
1 TGTATGGATACACTGCAAGG
451933 TGTATGGATAC
1 TGTATGGATAC
451944 CCTTTGACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 28 0.93
21 2 0.07
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.27
Consensus pattern (20 bp):
TGTATGGATACACTGCAAGG
Found at i:452220 original size:18 final size:19
Alignment explanation
Indices: 452167--452223 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
452157 ATGTTTAATG
* *
452167 AAAAATATACCAATTATTA
1 AAAAAGATACCAATTGTTA
**
452186 ACAAAAGAATATTAATTGTT-
1 A-AAAAG-ATACCAATTGTTA
452206 AAAAAGATACCAATTGTT
1 AAAAAGATACCAATTGTT
452224 GGAAAATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
18 10 0.33
19 6 0.20
20 5 0.17
21 9 0.30
ACGTcount: A:0.53, C:0.09, G:0.07, T:0.32
Consensus pattern (19 bp):
AAAAAGATACCAATTGTTA
Found at i:458510 original size:64 final size:63
Alignment explanation
Indices: 458442--458621 Score: 218
Period size: 65 Copynumber: 2.8 Consensus size: 63
458432 TTGGACTCTT
* * * * * *
458442 AGTGCATCGGTGCACTAAGAGTGCATCGATGCATAAAATGCATTCGATGTTTTGA-AATAGCTTG
1 AGTGCATCGATGCA-T-AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTG
* *
458506 AGTGCATCGATGCATTGTCTGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTG
1 AGTGCATCGATGCATAG--AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTG
*
458571 AGTGCATTGATGCATAGTATGTGCATCGATGCATCAAATGCATTCGATGTT
1 AGTGCATCGATGCATAG-A-GTGCATCGATGCATCAAATGCATTCGATGTT
458622 CAATTAATTT
Statistics
Matches: 100, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 46 0.46
65 52 0.52
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
AGTGCATCGATGCATAGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTG
Found at i:458603 original size:65 final size:64
Alignment explanation
Indices: 458462--458621 Score: 239
Period size: 65 Copynumber: 2.5 Consensus size: 64
458452 TGCACTAAGA
* * * * * * *
458462 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAAATAGCTTGAGTGCATCGATGCATTGTCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAACCCTGAGTGCATCGATGCATAGTAT
*
458526 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAACCCTGAGTGCATTGATGCATAGTAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAAACCCTGAGTGCATCGATGCATAGTAT
458591 GTGCATCGATGCATCAAATGCATTCGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
458622 CAATTAATTT
Statistics
Matches: 87, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 33 0.38
65 54 0.62
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAAACCCTGAGTGCATCGATGCATAGTAT
Found at i:460427 original size:15 final size:15
Alignment explanation
Indices: 460415--460444 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
460405 TCTTTATTTG
460415 TATATATTTTATTAT
1 TATATATTTTATTAT
460430 TATATATTTT-TTAT
1 TATATATTTTATTAT
460444 T
1 T
460445 TTTATGGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TATATATTTTATTAT
Found at i:460441 original size:17 final size:17
Alignment explanation
Indices: 460415--460449 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
460405 TCTTTATTTG
460415 TATATATTTTATTATTA
1 TATATATTTTATTATTA
* *
460432 TATATTTTTTATTTTTA
1 TATATATTTTATTATTA
460449 T
1 T
460450 GGTTATATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATATTTTATTATTA
Done.