Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000482.1 Hibiscus syriacus cultivar Beakdansim tig00000916_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: 2886609
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 16
Found at i:244817 original size:42 final size:41
Alignment explanation
Indices: 244717--244827 Score: 114
Period size: 42 Copynumber: 2.6 Consensus size: 41
244707 CCCGACTCAC
* * *
244717 CTGTCATCGTTCAAGAGGCCTCCCCTATCGTTCAAGAGGCCC
1 CTGTCATCGTTCAAGA-GCCTCCCCCACCGTTCAAGAGGCCA
* ** *
244759 CTATCATCCCTCAAGAGTCTCCTCCCACCGTTCAAGAGGCCA
1 CTGTCATCGTTCAAGAGCCTCC-CCCACCGTTCAAGAGGCCA
* *
244801 CTGTCATCGTTGAAGAGGCCTCTCCCA
1 CTGTCATCGTTCAAGA-GCCTCCCCCA
244828 ACATTCTAGA
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
41 5 0.09
42 45 0.83
43 4 0.07
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.23
Consensus pattern (41 bp):
CTGTCATCGTTCAAGAGCCTCCCCCACCGTTCAAGAGGCCA
Found at i:246227 original size:14 final size:14
Alignment explanation
Indices: 246208--246243 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
246198 ATTGTTTAAT
246208 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
246222 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
246236 TGATTTGT
1 TGATTTGT
246244 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:246388 original size:14 final size:14
Alignment explanation
Indices: 246369--246422 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
246359 GGAAATGACT
246369 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
246383 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
246402 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
246416 ATCGCAA
1 ATCGCAA
246423 TGCGAAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:246437 original size:34 final size:33
Alignment explanation
Indices: 246349--246444 Score: 147
Period size: 33 Copynumber: 2.8 Consensus size: 33
246339 AAAACAGATT
* **
246349 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
246383 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
246416 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
246445 CGAAACTAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 32 0.55
34 26 0.45
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:246440 original size:20 final size:19
Alignment explanation
Indices: 246382--246449 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 19
246372 GCAACGAGAG
246382 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
246401 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
246415 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
246435 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
246450 CTAAATTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
19 12 0.30
20 13 0.32
ACGTcount: A:0.47, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:246516 original size:33 final size:34
Alignment explanation
Indices: 246459--246531 Score: 130
Period size: 33 Copynumber: 2.2 Consensus size: 34
246449 ACTAAATTCG
*
246459 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCAATTCTCT
246493 CGTTGCGATTTTCA-TTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCAATTCTCT
246526 CGTTGC
1 CGTTGC
246532 AATAGTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 24 0.63
34 14 0.37
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.45
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCAATTCTCT
Found at i:246543 original size:33 final size:33
Alignment explanation
Indices: 246459--246543 Score: 100
Period size: 33 Copynumber: 2.5 Consensus size: 33
246449 ACTAAATTCG
* * *
246459 CGTTGCGATTTTCATTTTCGCATTGCGATTCTCT
1 CGTTGCAATGTTCA-TTTCGCATTGCAATTCTCT
* *
246493 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCAATGTTCATTTCGCATTGCAATTCTCT
246526 CGTTGCAATAGTT-ATTTC
1 CGTTGCAAT-GTTCATTTC
246544 CGCTTTGCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
33 31 0.66
34 16 0.34
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.46
Consensus pattern (33 bp):
CGTTGCAATGTTCATTTCGCATTGCAATTCTCT
Found at i:246577 original size:40 final size:40
Alignment explanation
Indices: 246517--246614 Score: 110
Period size: 40 Copynumber: 2.4 Consensus size: 40
246507 TTTCGCATTG
* * * *
246517 CAATTCTCTCGTTGCAATAGTTATTTCCGCT-TTGCGATAGT
1 CAATTC-CGCGTTGCGATAGTCATTTCC-ATGTTGCGATAGT
246558 CAATTCCGCGTTGCGATAGTCATTTCCATGTTGCGATAGT
1 CAATTCCGCGTTGCGATAGTCATTTCCATGTTGCGATAGT
*
246598 CATATT-CGTGTTGCGAT
1 CA-ATTCCGCGTTGCGAT
246615 TTCTGTGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
39 1 0.02
40 40 0.80
41 9 0.18
ACGTcount: A:0.19, C:0.21, G:0.20, T:0.39
Consensus pattern (40 bp):
CAATTCCGCGTTGCGATAGTCATTTCCATGTTGCGATAGT
Found at i:246609 original size:20 final size:21
Alignment explanation
Indices: 246527--246614 Score: 96
Period size: 20 Copynumber: 4.4 Consensus size: 21
246517 CAATTCTCTC
* *
246527 GTTGCAATAGTTAT-TTCCGCT
1 GTTGCGATAGTCATATTCCG-T
*
246548 -TTGCGATAGTCA-ATTCCGC
1 GTTGCGATAGTCATATTCCGT
*
246567 GTTGCGATAGTCAT-TTCCAT
1 GTTGCGATAGTCATATTCCGT
246587 GTTGCGATAGTCATATT-CGT
1 GTTGCGATAGTCATATTCCGT
246607 GTTGCGAT
1 GTTGCGAT
246615 TTCTGTGTTG
Statistics
Matches: 57, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
20 55 0.96
21 2 0.04
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (21 bp):
GTTGCGATAGTCATATTCCGT
Found at i:249071 original size:24 final size:24
Alignment explanation
Indices: 249039--249091 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
249029 AAAAATCATC
249039 AAAA-TCCGAGTATTGACCAAGAT
1 AAAATTCCGAGTATTGACCAAGAT
249062 AAAATTCCGAGTATTGACCAAGAT
1 AAAATTCCGAGTATTGACCAAGAT
*
249086 CAAATT
1 AAAATT
249092 TCGAATACTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (24 bp):
AAAATTCCGAGTATTGACCAAGAT
Found at i:249103 original size:24 final size:24
Alignment explanation
Indices: 249039--249103 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
249029 AAAAATCATC
* *
249039 AAAA-TCCGAGTATTGACCAAGAT
1 AAAATTCCGAATACTGACCAAGAT
* *
249062 AAAATTCCGAGTATTGACCAAGAT
1 AAAATTCCGAATACTGACCAAGAT
* *
249086 CAAATTTCGAATACTGAC
1 AAAATTCCGAATACTGAC
249104 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
23 4 0.11
24 33 0.89
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.25
Consensus pattern (24 bp):
AAAATTCCGAATACTGACCAAGAT
Found at i:249954 original size:20 final size:20
Alignment explanation
Indices: 249929--249975 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
249919 AAATTTAGTA
*
249929 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
249949 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
249969 TTGCGAT
1 TTGCGAT
249976 TTACGTATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:249985 original size:20 final size:20
Alignment explanation
Indices: 249962--250114 Score: 252
Period size: 20 Copynumber: 7.7 Consensus size: 20
249952 CGATAGTCAG
*
249962 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
249982 ATTCACATTACGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
250002 ATTCGCATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
*
250022 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
250042 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
250062 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
250082 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
250102 ATTCGCATTGCGA
1 ATTCGCATTGCGA
250115 ATTAGGAAAA
Statistics
Matches: 122, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 122 1.00
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:251285 original size:28 final size:30
Alignment explanation
Indices: 251224--251285 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 30
251214 ATTATCTAAT
* ***
251224 TAATATTTAATGACTTTATGTTTTTAATTG
1 TAATATTTAATGACGTTATGTTTTTAAAAA
251254 TAATATTTAATGA-GTT-TGTTTTTAAAAA
1 TAATATTTAATGACGTTATGTTTTTAAAAA
251282 TAAT
1 TAAT
251286 GGTATATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 13 0.46
29 2 0.07
30 13 0.46
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.53
Consensus pattern (30 bp):
TAATATTTAATGACGTTATGTTTTTAAAAA
Found at i:251608 original size:12 final size:14
Alignment explanation
Indices: 251585--251623 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
251575 CAGTGACTGA
251585 AAAAATATATATTG
1 AAAAATATATATTG
251599 AAAAATATATATTG
1 AAAAATATATATTG
251613 AAAAATATATA
1 AAAAATATATA
251624 AATAAAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (14 bp):
AAAAATATATATTG
Found at i:251957 original size:36 final size:38
Alignment explanation
Indices: 251911--251993 Score: 100
Period size: 36 Copynumber: 2.2 Consensus size: 38
251901 TAAAATAGTC
*
251911 ATTTCTAATGCTAG-TGGAAAAACCTAA-CTTGAGCATT
1 ATTTCCAATGCT-GTTGGAAAAACCTAATCTTGAGCATT
* *
251948 -TTTCCAATGCTGTTGGAAATACCTAATTTTGAGCATT
1 ATTTCCAATGCTGTTGGAAAAACCTAATCTTGAGCATT
*
251985 AATTCCAAT
1 ATTTCCAAT
251994 AGTCAATTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
35 1 0.03
36 22 0.56
37 9 0.23
38 7 0.18
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (38 bp):
ATTTCCAATGCTGTTGGAAAAACCTAATCTTGAGCATT
Found at i:252596 original size:31 final size:31
Alignment explanation
Indices: 252561--252621 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
252551 AATTCGATGA
252561 ATTCAATATGTCATTCTCACTAGGAACTCCC
1 ATTCAATATGTCATTCTCACTAGGAACTCCC
*
252592 ATTCAATATGTTATTCTCACTAGGAACTCC
1 ATTCAATATGTCATTCTCACTAGGAACTCC
252622 AAAACTCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (31 bp):
ATTCAATATGTCATTCTCACTAGGAACTCCC
Found at i:256878 original size:36 final size:38
Alignment explanation
Indices: 256834--256916 Score: 116
Period size: 36 Copynumber: 2.2 Consensus size: 38
256824 GAAAATAATC
*
256834 ATTTCCAATGCTAGTGGAAAAACCTAA-CTTGAGCATT
1 ATTTCCAATGCCAGTGGAAAAACCTAATCTTGAGCATT
* *
256871 -TTTCCAATGCCAGTGGAAATACCTAATTTTGAGCATT
1 ATTTCCAATGCCAGTGGAAAAACCTAATCTTGAGCATT
*
256908 AATTCCAAT
1 ATTTCCAAT
256917 AGTCAATTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 24 0.60
37 9 0.22
38 7 0.17
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (38 bp):
ATTTCCAATGCCAGTGGAAAAACCTAATCTTGAGCATT
Found at i:265556 original size:12 final size:13
Alignment explanation
Indices: 265537--265567 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
265527 TTAATTTGAT
265537 TAAAAAAATTAAA
1 TAAAAAAATTAAA
265550 TAAAAAAATTAAA
1 TAAAAAAATTAAA
265563 TAAAA
1 TAAAA
265568 TTTAATGGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAAAATTAAA
Found at i:268896 original size:3 final size:3
Alignment explanation
Indices: 268888--268960 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
268878 TACCCATATC
*
268888 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
268936 ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
268961 AATATATTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:269499 original size:28 final size:29
Alignment explanation
Indices: 269450--269504 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
269440 AAAAAAAAGA
* *
269450 GGAGAGACAAAAAAAACCGAGACAGAACC
1 GGAGAGACAAAAAAAACAGAGAAAGAACC
269479 GGAGAGA-AAAAAAAACAGAGAAAGAA
1 GGAGAGACAAAAAAAACAGAGAAAGAA
269505 AAAAAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 17 0.71
29 7 0.29
ACGTcount: A:0.62, C:0.13, G:0.25, T:0.00
Consensus pattern (29 bp):
GGAGAGACAAAAAAAACAGAGAAAGAACC
Found at i:270461 original size:13 final size:13
Alignment explanation
Indices: 270445--270491 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
270435 ATATAATAAA
270445 TAAATATTTATTT
1 TAAATATTTATTT
*
270458 TAAATAAATTATTT
1 TAAAT-ATTTATTT
270472 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
270485 TCAATAT
1 TAAATAT
270492 CAAAGAACAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:271143 original size:4 final size:4
Alignment explanation
Indices: 271136--271164 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
271126 TCTTTTCAAA
271136 TTAT TTAT TTAT TTAT TTAT TTA- TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
271165 TTATAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:271153 original size:12 final size:11
Alignment explanation
Indices: 271135--271177 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
271125 TTCTTTTCAA
271135 ATTATTTATTT
1 ATTATTTATTT
271146 ATTTATTTATTT
1 A-TTATTTATTT
271158 ATTATTT-TTAT
1 ATTATTTATT-T
*
271169 AATATTTAT
1 ATTATTTAT
271178 ATGTTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
10 2 0.07
11 14 0.50
12 12 0.43
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (11 bp):
ATTATTTATTT
Found at i:271192 original size:18 final size:18
Alignment explanation
Indices: 271136--271193 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
271126 TCTTTTCAAA
*
271136 TTATTTATT-TATTTA-T
1 TTATTTATTATTTTTATT
*
271152 TTATTTATTATTTTTATA
1 TTATTTATTATTTTTATT
*
271170 ATATTTA-TATGTTTTATT
1 TTATTTATTAT-TTTTATT
271188 TTATTT
1 TTATTT
271194 GCAAGTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
16 9 0.26
17 8 0.24
18 17 0.50
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (18 bp):
TTATTTATTATTTTTATT
Found at i:271215 original size:13 final size:15
Alignment explanation
Indices: 271184--271220 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
271174 TTATATGTTT
271184 TATTTTATTTGCAAG
1 TATTTTATTTGCAAG
271199 TATTTTATTT-C-AG
1 TATTTTATTTGCAAG
271212 TA-TTTATTT
1 TATTTTATTT
271221 TTCTGTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 7 0.32
13 4 0.18
14 1 0.05
15 10 0.45
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.62
Consensus pattern (15 bp):
TATTTTATTTGCAAG
Found at i:281643 original size:18 final size:18
Alignment explanation
Indices: 281620--281654 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
281610 CTTGAAGAAG
281620 AAAAAAAAAGAAAAAAGA
1 AAAAAAAAAGAAAAAAGA
281638 AAAAAAAAAGAAAAAAG
1 AAAAAAAAAGAAAAAAG
281655 GGGGGTCAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAAGA
Found at i:281644 original size:11 final size:11
Alignment explanation
Indices: 281620--281653 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
281610 CTTGAAGAAG
*
281620 AAAAAA-AAAG
1 AAAAAAGAAAA
281630 AAAAAAGAAAA
1 AAAAAAGAAAA
281641 AAAAAAGAAAA
1 AAAAAAGAAAA
281652 AA
1 AA
281654 GGGGGGTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 6 0.27
11 16 0.73
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:282017 original size:19 final size:20
Alignment explanation
Indices: 281984--282025 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
281974 TTCAAGTTCA
*
281984 ATTTATTGGAGATTCAATTT
1 ATTTATTGGAAATTCAATTT
282004 ATTT-TTGGAAATTCAATTT
1 ATTTATTGGAAATTCAATTT
282023 ATT
1 ATT
282026 CTTTTCTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (20 bp):
ATTTATTGGAAATTCAATTT
Found at i:283217 original size:84 final size:84
Alignment explanation
Indices: 282775--283207 Score: 791
Period size: 84 Copynumber: 5.2 Consensus size: 84
282765 ATATCTTAGT
282775 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
282839 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
282858 CCAATCATTGAATTTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
282922 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
282941 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
283006 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
*
283025 CCAATCATTGAATTTGGAAGATGAATTTGCTTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
283090 CTGATCTGATTTGGCAGAA
66 CTGATCTGATTTGGCAGAA
283109 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
1 CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
* *
283174 CTAATCTG-GTTGGACAGAA
66 CTGATCTGATTTGG-CAGAA
*
283193 CCAATCGTTGGAATT
1 CCAATCATT-GAATT
283208 AAAAGATGAA
Statistics
Matches: 342, Mismatches: 5, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
83 117 0.34
84 220 0.64
85 5 0.01
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.36
Consensus pattern (84 bp):
CCAATCATTGAATTTGGAAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTAT
CTGATCTGATTTGGCAGAA
Found at i:284018 original size:113 final size:113
Alignment explanation
Indices: 283822--284945 Score: 1572
Period size: 113 Copynumber: 10.0 Consensus size: 113
283812 GCAAAGATTC
* **
283822 AAATCTATCAATTGATGGATTATTTTTTGAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
283887 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
283935 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
284000 AAGAAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTTGCTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * *** * *
284048 GAAT-TCATCA-TCTGATGGATCAACATTGCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTG
1 AAATCT-ATCACT-TGATGGATTATTTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTG
*
284110 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
284161 AAATCTATCACTTGATGGATTA-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
284225 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * *** *
284273 GAAT-TCATCA-TTGGATGGATCAACATTGCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 AAATCT-ATCACTT-GATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * *
284336 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGTTT
64 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * *
284386 GAAT-TCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCT-ATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* *
284450 GAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTAAT-CTG
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT--TGCTT
* * * *
284500 AATTC-ATCACTGGATGGAATATTTTTTTCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
284564 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * *
284612 GAAT-TCATCACTTGATGGATTATTTTTGCCAGAGAAGGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCT-ATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* *
284676 GAAGGAAGAAGAAGTTCATAATAAGAAGAATTTGTTCAACCTTTAAT-CTG
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT--TGCTT
* *
284726 AATTC-ATCACTGGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
284790 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTACCT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * ***
284838 GAAT-TCATCAATTGATGGATCAGCCTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
1 AAATCT-ATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
284902 GAAGGAAGAAGAAGTTCATAATGAGAAGAGTTTGTTCAACCTTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTT
284946 GTTTGATGCT
Statistics
Matches: 909, Mismatches: 80, Indels: 44
0.88 0.08 0.04
Matches are distributed among these distances:
111 5 0.01
112 104 0.11
113 788 0.87
114 10 0.01
115 2 0.00
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (113 bp):
AAATCTATCACTTGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
Found at i:285275 original size:3 final size:3
Alignment explanation
Indices: 285267--285339 Score: 128
Period size: 3 Copynumber: 24.3 Consensus size: 3
285257 TACCCATATC
*
285267 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
285315 ATT ATC ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
285340 AATATATTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:285886 original size:29 final size:29
Alignment explanation
Indices: 285844--285899 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
285834 AAAAAAAAGA
* * *
285844 GGAGAGACAAAAAAAACCGAGACAGAACC
1 GGAGAGAAAAAAAAAACAGAGAAAGAACC
285873 GGAGAGAAAAAAAAAACAGAGAAAGAA
1 GGAGAGAAAAAAAAAACAGAGAAAGAA
285900 AAAAAAAACA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.62, C:0.12, G:0.25, T:0.00
Consensus pattern (29 bp):
GGAGAGAAAAAAAAAACAGAGAAAGAACC
Found at i:285895 original size:15 final size:16
Alignment explanation
Indices: 285875--285904 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
285865 ACAGAACCGG
285875 AGAGAAA-AAAAAAAC
1 AGAGAAAGAAAAAAAC
285890 AGAGAAAGAAAAAAA
1 AGAGAAAGAAAAAAA
285905 AAACAACAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AGAGAAAGAAAAAAAC
Found at i:286859 original size:13 final size:13
Alignment explanation
Indices: 286843--286889 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
286833 ATATAATAAA
286843 TAAATATTTATTT
1 TAAATATTTATTT
*
286856 TAAATAAATTATTT
1 TAAAT-ATTTATTT
286870 T-AATATTTAGTTT
1 TAAATATTTA-TTT
*
286883 TCAATAT
1 TAAATAT
286890 CAAAGAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.41
14 13 0.45
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:287436 original size:12 final size:12
Alignment explanation
Indices: 287419--287500 Score: 69
Period size: 14 Copynumber: 6.5 Consensus size: 12
287409 CGGTTACGAC
287419 AATTTTAATATT
1 AATTTTAATATT
287431 AATTTTTTAA-A-T
1 AA--TTTTAATATT
* *
287443 AAATTAAATATT
1 AATTTTAATATT
287455 AATTTTTTAATATT
1 AA--TTTTAATATT
*
287469 ATATTATAGATATT
1 A-ATTTTA-ATATT
287483 AATTTTAATATT
1 AATTTTAATATT
287495 AATTTT
1 AATTTT
287501 TTAAATAAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 16
0.72 0.08 0.21
Matches are distributed among these distances:
10 4 0.07
11 1 0.02
12 19 0.34
13 10 0.18
14 21 0.38
15 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (12 bp):
AATTTTAATATT
Found at i:287474 original size:26 final size:27
Alignment explanation
Indices: 287419--287496 Score: 94
Period size: 26 Copynumber: 3.0 Consensus size: 27
287409 CGGTTACGAC
*
287419 AATTTTAATATTAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
287444 AATTA-AATATTAATTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
287470 TATTATAGATATTAA--TTTTAATATTA
1 AATTATA-ATATTAATTTTTTAATATTA
287496 A
1 A
287497 TTTTTTAAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
24 16 0.35
25 5 0.11
26 17 0.37
27 1 0.02
28 7 0.15
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:287487 original size:64 final size:65
Alignment explanation
Indices: 287419--287554 Score: 256
Period size: 64 Copynumber: 2.1 Consensus size: 65
287409 CGGTTACGAC
287419 AATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATA-TT
1 AATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTT
*
287483 AATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTTTATTATAGATATTT
1 AATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTT
287548 AATTTTA
1 AATTTTA
287555 TATCATATAA
Statistics
Matches: 70, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 61 0.87
65 9 0.13
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (65 bp):
AATTTTAATATTAATTTTTTAAATAAATTAAATATTAATTTTTTAATATTATATTATAGATATTT
Found at i:287499 original size:40 final size:36
Alignment explanation
Indices: 287449--287524 Score: 107
Period size: 40 Copynumber: 2.0 Consensus size: 36
287439 AAATAAATTA
*
287449 AATATTAATTTTTTAATATTATATTATAGATATTAATTTT
1 AATATTAATTTTTTAA-A-TAAATTA-A-ATATTAATTTT
287489 AATATTAATTTTTTAAATAAATTAAATATTAATTTT
1 AATATTAATTTTTTAAATAAATTAAATATTAATTTT
287525 TTAATATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
36 11 0.31
37 1 0.03
38 6 0.17
39 1 0.03
40 16 0.46
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (36 bp):
AATATTAATTTTTTAAATAAATTAAATATTAATTTT
Found at i:287609 original size:20 final size:19
Alignment explanation
Indices: 287549--287610 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
287539 TAGATATTTA
*
287549 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
287568 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
287586 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
287606 ATTTT
1 ATTTT
287611 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:291159 original size:77 final size:77
Alignment explanation
Indices: 291066--291219 Score: 281
Period size: 77 Copynumber: 2.0 Consensus size: 77
291056 AATAAAGTAA
* * *
291066 TCAAAATAAGAATAATTTGAAATTTGAGTAACTAAATTGAATATTGTTAAAATTGGGTGACCAAA
1 TCAAAATAAGAATAATTTGAAATTTAAGTAACTAAATTGAATATTGTTAAAATTGAGTGACAAAA
291131 ACAAGAACATAG
66 ACAAGAACATAG
291143 TCAAAATAAGAATAATTTGAAATTTAAGTAACTAAATTGAATATTGTTAAAATTGAGTGACAAAA
1 TCAAAATAAGAATAATTTGAAATTTAAGTAACTAAATTGAATATTGTTAAAATTGAGTGACAAAA
291208 ACAAGAACATAG
66 ACAAGAACATAG
291220 GTAAAGTTAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 74 1.00
ACGTcount: A:0.50, C:0.07, G:0.14, T:0.29
Consensus pattern (77 bp):
TCAAAATAAGAATAATTTGAAATTTAAGTAACTAAATTGAATATTGTTAAAATTGAGTGACAAAA
ACAAGAACATAG
Found at i:291440 original size:2 final size:2
Alignment explanation
Indices: 291433--291462 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
291423 AAATAATTAT
291433 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
291463 TAATAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:297592 original size:4 final size:4
Alignment explanation
Indices: 297583--297609 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
297573 TCTTCATTAC
297583 GTAT GTAT GTAT GTAT GTAT GTAT GTA
1 GTAT GTAT GTAT GTAT GTAT GTAT GTA
297610 GTGATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (4 bp):
GTAT
Found at i:298884 original size:43 final size:41
Alignment explanation
Indices: 298829--299212 Score: 315
Period size: 43 Copynumber: 8.9 Consensus size: 41
298819 GGTTTTCACA
* *
298829 AAAAACGCCGCAATAAGTATTGATATTTAGCGGCGTTTGTGT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT-T
* *
298871 GAAAAACGTCGCAATAGGTGTTGATATTTAGTGGCGTTTGTTAT
1 -AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTG-T-T
* *
298915 AAAAACGCAGTAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT--T
* *
298958 AAAAACGCCGCAATAGGTGTTGATATTTAACAGCGTTT-TT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTT
* * * * * *
298998 CAACAAACGCCGTAATAGGTATTGATATTTAGTGACTTTTTTTTTTAT
1 -AA-AAACGCCGCAATAGGTGTTGATATTTAGCGGC----GTTTGT-T
* * *
299046 AAAAACGCCGCAAAAGGTGTTGATTTTTAACGGCGTTTGTCAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT--T
* * * *
299089 AAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTCTC
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTT
* * *
299130 AGATAAACGCCGTAATATGT-TATGATGTTTAGCGGCGTTTTTTGTT
1 A-A-AAACGCCGCAATAGGTGT-TGATATTTAGCGGCG---TTTGTT
* * *
299176 -AAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
299213 CTACTAAAAA
Statistics
Matches: 276, Mismatches: 47, Indels: 39
0.76 0.13 0.11
Matches are distributed among these distances:
40 4 0.01
41 3 0.01
42 34 0.12
43 195 0.71
44 4 0.01
46 32 0.12
47 3 0.01
48 1 0.00
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (41 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTT
Found at i:298974 original size:86 final size:86
Alignment explanation
Indices: 298829--299212 Score: 371
Period size: 86 Copynumber: 4.4 Consensus size: 86
298819 GGTTTTCACA
* * * *
298829 AAAAACGCCGCAATAAGTATTGATATTTAGCGGCGTTTGT-GTGAAAAACGTCGCAATAGGTGTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAT-AAAAACGCCGCAATAGGTGTT
**
298893 GATATTTAGTGGCGTTTGTTAT
65 GATATTTAACGGCGTTTGTTAT
* *
298915 AAAAACGCAGTAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACGCCGCAATAGGTGTTG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACGCCGCAATAGGTGTTG
*
298980 ATATTTAACAGCGTTT-TTCA-
66 ATATTTAACGGCGTTTGTT-AT
* * * * * * * * *
299000 ACAAACGCCGTAATAGGTATTGATATTTAGTGACTTTTTTTTTTATAAAAACGCCGCAAAAGGTG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGC---GTTTGTCATAAAAACGCCGCAATAGGTG
* *
299065 TTGATTTTTAACGGCGTTTGTCAT
63 TTGATATTTAACGGCGTTTGTTAT
* * * * * * *
299089 AAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTCTCAGATAAACGCCGTAATATGT-TAT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACGCCGCAATAGGTGT-T
* * * *
299153 GATGTTTAGCGGCGTTTTTTGT
65 GATATTTAACGGCGTTTGTTAT
* * * *
299175 TAAAACGCCGCAGTAGGTGTTGATGTTTTGCGGCGTTT
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
299213 CTACTAAAAA
Statistics
Matches: 243, Mismatches: 47, Indels: 16
0.79 0.15 0.05
Matches are distributed among these distances:
85 32 0.13
86 140 0.58
87 1 0.00
88 42 0.17
89 28 0.12
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (86 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCATAAAAACGCCGCAATAGGTGTTG
ATATTTAACGGCGTTTGTTAT
Found at i:299075 original size:88 final size:89
Alignment explanation
Indices: 298872--299118 Score: 259
Period size: 88 Copynumber: 2.8 Consensus size: 89
298862 CGTTTGTGTG
* * *** * * * * *
298872 AAAAACGTCGCAATAGGTGTTGATATTTAGTGGCGTTTGTTATAAAAACGCAGTAATAGGTGTTG
1 AAAAACGCCGCAAAAGGTGTTGATATTTAACAGCGTTTGTCATAAAAACGCCGCAATAGGTATTA
* * * * *
298937 ATATTTAGCGGC---GTTTGTCAT
66 ATATTTAGTGACTTTTTTTTTTAT
* * * * *
298958 AAAAACGCCGCAATAGGTGTTGATATTTAACAGCGTTTTTCA-ACAAACGCCGTAATAGGTATTG
1 AAAAACGCCGCAAAAGGTGTTGATATTTAACAGCGTTTGTCATAAAAACGCCGCAATAGGTATTA
299022 ATATTTAGTGACTTTTTTTTTTAT
66 ATATTTAGTGACTTTTTTTTTTAT
* * *
299046 AAAAACGCCGCAAAAGGTGTTGATTTTTAACGGCGTTTGTCATAAAAACGCCGCAATAGGTGTTA
1 AAAAACGCCGCAAAAGGTGTTGATATTTAACAGCGTTTGTCATAAAAACGCCGCAATAGGTATTA
299111 ATATTTAG
66 ATATTTAG
299119 CAGCGTTTCT
Statistics
Matches: 135, Mismatches: 22, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
85 29 0.21
86 36 0.27
88 44 0.33
89 26 0.19
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.34
Consensus pattern (89 bp):
AAAAACGCCGCAAAAGGTGTTGATATTTAACAGCGTTTGTCATAAAAACGCCGCAATAGGTATTA
ATATTTAGTGACTTTTTTTTTTAT
Found at i:299084 original size:131 final size:127
Alignment explanation
Indices: 298829--299146 Score: 402
Period size: 131 Copynumber: 2.4 Consensus size: 127
298819 GGTTTTCACA
* * * * * * *
298829 AAAAACGCCGCAATAAGTATTGATATTTAGCGGCGTTTGTGTGAAAAACGTCGCAATAGGTGTTG
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCAGCGTTT-T-TCAAAAACGCCGTAATAGGTATTG
* * * *
298894 ATATTTAGTGGCGTTTGTTATAAAAACGCAGTAATAGGTGTTGATATTTAGCGGCGTTTGTCAT
64 ATATTTAGTGACGTTTGTTATAAAAACGCAGCAAAAGGTGTTGATATTTAACGGCGTTTGTCAT
*
298958 AAAAACGCCGCAATAGGTGTTGATATTTAACAGCGTTTTTCAACAAACGCCGTAATAGGTATTGA
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCAGCGTTTTTCAA-AAACGCCGTAATAGGTATTGA
* * * *
299023 TATTTAGTGACTTTTTTTTTTATAAAAACGCCGCAAAAGGTGTTGATTTTTAACGGCGTTTGTCA
65 TATTTAGTGAC---GTTTGTTATAAAAACGCAGCAAAAGGTGTTGATATTTAACGGCGTTTGTCA
299088 T
127 T
* *
299089 AAAAACGCCGCAATAGGTGTTAATATTTAGCAGCGTTTCTCAGATAAACGCCGTAATA
1 AAAAACGCCGCAATAGGTGTTGATATTTAGCAGCGTTTTTCA-A-AAACGCCGTAATA
299147 TGTTATGATG
Statistics
Matches: 164, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
127 3 0.02
128 29 0.18
129 34 0.21
131 84 0.51
132 14 0.09
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (127 bp):
AAAAACGCCGCAATAGGTGTTGATATTTAGCAGCGTTTTTCAAAAACGCCGTAATAGGTATTGAT
ATTTAGTGACGTTTGTTATAAAAACGCAGCAAAAGGTGTTGATATTTAACGGCGTTTGTCAT
Found at i:299653 original size:21 final size:21
Alignment explanation
Indices: 299629--299668 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
299619 TGATATGCTA
*
299629 CTTCTCTCTGTGCTGCCGCTG
1 CTTCTCTCTATGCTGCCGCTG
299650 CTTCTCTCTATGCTGCCGC
1 CTTCTCTCTATGCTGCCGC
299669 AAATTCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.03, C:0.40, G:0.20, T:0.38
Consensus pattern (21 bp):
CTTCTCTCTATGCTGCCGCTG
Found at i:299726 original size:21 final size:21
Alignment explanation
Indices: 299632--299729 Score: 63
Period size: 21 Copynumber: 4.7 Consensus size: 21
299622 TATGCTACTT
* * *
299632 CTCTCTGTGCTGCCGCTGCTT
1 CTCTCTCTGCTTCCGCTGCTG
* * *** *
299653 CTCTCTATGCTGCCGCAAATT
1 CTCTCTCTGCTTCCGCTGCTG
*
299674 CTTTCTCTGCTTCCGCTGCTG
1 CTCTCTCTGCTTCCGCTGCTG
* * *
299695 CTCTGGT-TGCTTCTGTTGCTG
1 CTCT-CTCTGCTTCCGCTGCTG
299716 CTCTCTCTGCTTCC
1 CTCTCTCTGCTTCC
299730 CTTGTTTTAT
Statistics
Matches: 58, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
20 1 0.02
21 56 0.97
22 1 0.02
ACGTcount: A:0.04, C:0.36, G:0.19, T:0.41
Consensus pattern (21 bp):
CTCTCTCTGCTTCCGCTGCTG
Found at i:303827 original size:43 final size:43
Alignment explanation
Indices: 303770--303858 Score: 144
Period size: 43 Copynumber: 2.1 Consensus size: 43
303760 GCGTTTTTAT
* *
303770 AAAAACGCCGCAAAATATTATATCTATTGCGGTGTTTATCTTAA
1 AAAAACGCCACAAAATATTATATCTATTGCGGCGTTTATC-TAA
303814 AAAAAC-CCACAAAATATTATATCTATTGCGGCGTTTATCTAA
1 AAAAACGCCACAAAATATTATATCTATTGCGGCGTTTATCTAA
303856 AAA
1 AAA
303859 TGCCACTAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 6 0.14
43 31 0.72
44 6 0.14
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.31
Consensus pattern (43 bp):
AAAAACGCCACAAAATATTATATCTATTGCGGCGTTTATCTAA
Found at i:303932 original size:41 final size:41
Alignment explanation
Indices: 303835--304180 Score: 329
Period size: 41 Copynumber: 8.4 Consensus size: 41
303825 AAATATTATA
* * * * *
303835 TCTATTGCGGCGTTTATCTAAAAATGCCACTAAGGGTACGAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAA-AGTACGAG
* * * *
303877 TCTATAGCAGCGTTTGTATAAAAATGCCAATAAAGTACAAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* **
303918 TCTATAGCGGCGTTTATATAAAAACGCTGCTAAAGTACGAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* * * * *
303959 TATTTAGCGGCGTTT-TCATTCAAAACACCACTAAAGTATGAG
1 TCTATAGCGGCGTTTGT-A-TAAAAACGCCACTAAAGTACGAG
* * * * *
304001 TTTATAGCAGTGTTTAG-ATTCAAAACGCCACTAAAGTATGAG
1 TCTATAGCGGCGTTT-GTA-TAAAAACGCCACTAAAGTACGAG
* * *
304043 TATATAGCGGCGTTTGTATAGAAACGCCACTAAAGTACTAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* * * *
304084 TATATAGCGGTGTTTGTATAAAAACGCCACTAACGTACGAT
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* *
304125 TCTATAGCGGCGTTTGTATAAAAATGCCACTAAAGTATGTA-
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACG-AG
*
304166 CCTATAGCGGCGTTT
1 TCTATAGCGGCGTTT
304181 CTGGATACAA
Statistics
Matches: 254, Mismatches: 44, Indels: 13
0.82 0.14 0.04
Matches are distributed among these distances:
40 1 0.00
41 158 0.62
42 95 0.37
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (41 bp):
TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
Found at i:304193 original size:125 final size:123
Alignment explanation
Indices: 303841--304200 Score: 335
Period size: 125 Copynumber: 2.9 Consensus size: 123
303831 TATATCTATT
* * *
303841 GCGGCG-TTT-ATCTAAAAATGCCACTAAGGGTACGAGTCTATAGCAGCGTTTGTATAAAAATGC
1 GCGGCGTTTTCAT-TAAAAACGCCACTAA-AGTACGATTCTATAGCAGCGTTTGTATAAAAATGC
* * * *
303904 CAATAAAGTACAAGT-CTATAGCGGCGTTTAT-ATAAAAACGCTGCTAAAGTACGAGTATTTA
64 CACTAAAGT--ATGTACTATAGCGGCGTTT-TGATAAAAACGCCGCTAAAGTACGAGTATATA
* * * * * *
303965 GCGGCGTTTTCATTCAAAACACCACTAAAGTATGAGTT-TATAGCAGTGTTTAG-ATTCAAAACG
1 GCGGCGTTTTCATTAAAAACGCCACTAAAGTACGA-TTCTATAGCAGCGTTT-GTA-TAAAAATG
* * *
304028 CCACTAAAGTATGAGTA-TATAGCGGCG-TTTGTATAGAAACGCCACTAAAGTACTAGTATATA
63 CCACTAAAGTAT--GTACTATAGCGGCGTTTTG-ATAAAAACGCCGCTAAAGTACGAGTATATA
* * *
304090 GCGGTGTTTGT-A-TAAAAACGCCACTAACGTACGATTCTATAGCGGCGTTTGTATAAAAATGCC
1 GCGGCGTTT-TCATTAAAAACGCCACTAAAGTACGATTCTATAGCAGCGTTTGTATAAAAATGCC
*
304153 ACTAAAGTATGTACCTATAGCGGCGTTTCTGGATACAAACGCCGCTAA
65 ACTAAAGTATGTA-CTATAGCGGCGTTT-T-GATAAAAACGCCGCTAA
304201 TTACCTTTTA
Statistics
Matches: 191, Mismatches: 27, Indels: 35
0.75 0.11 0.14
Matches are distributed among these distances:
121 3 0.02
123 33 0.17
124 58 0.30
125 93 0.49
126 4 0.02
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (123 bp):
GCGGCGTTTTCATTAAAAACGCCACTAAAGTACGATTCTATAGCAGCGTTTGTATAAAAATGCCA
CTAAAGTATGTACTATAGCGGCGTTTTGATAAAAACGCCGCTAAAGTACGAGTATATA
Found at i:304195 original size:166 final size:167
Alignment explanation
Indices: 303855--304180 Score: 372
Period size: 166 Copynumber: 2.0 Consensus size: 167
303845 CGTTTATCTA
* * * * *
303855 AAAATGCCACTAAGGGTACGAGTCTATAGCAGCGTTTGTATAAAAATGCCAATAAAGTACAAGTC
1 AAAACGCCACTAAGAGTACGAGTATATAGCAGCGTTTGTATAAAAACGCCAATAAAGTACAAGTA
** * *
303920 TATAGCGGCGTTTATATAAAAACGCTGCTAAAGTACGAGTATTTAGCGGCGTTTTCATTCAAAAC
66 TATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATATAGCGGCGTTTTCATTAAAAAC
** * *
303985 ACCACTAAAGTATGAGTTTATAGCAGTGTTTAGATTC
131 ACCACTAAAGTATGAGCCTATAGCAGCGTTTAGATAC
* * * * *
304022 AAAACGCCACTAA-AGTATGAGTATATAGCGGCGTTTGTATAGAAACGCCACTAAAGTACTAGTA
1 AAAACGCCACTAAGAGTACGAGTATATAGCAGCGTTTGTATAAAAACGCCAATAAAGTACAAGTA
* * * * *
304086 TATAGCGGTGTTTGTATAAAAACGCCACTAACGTACGATTCTATAGCGGCGTTTGT-A-TAAAAA
66 TATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATATAGCGGCGTTT-TCATTAAAAA
** *
304149 TGCCACTAAAGTATGTA-CCTATAGCGGCGTTT
130 CACCACTAAAGTATG-AGCCTATAGCAGCGTTT
304181 CTGGATACAA
Statistics
Matches: 132, Mismatches: 25, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
165 29 0.22
166 90 0.68
167 13 0.10
ACGTcount: A:0.35, C:0.17, G:0.20, T:0.28
Consensus pattern (167 bp):
AAAACGCCACTAAGAGTACGAGTATATAGCAGCGTTTGTATAAAAACGCCAATAAAGTACAAGTA
TATAGCGGCGTTTATATAAAAACGCCACTAAAGTACGAGTATATAGCGGCGTTTTCATTAAAAAC
ACCACTAAAGTATGAGCCTATAGCAGCGTTTAGATAC
Found at i:305482 original size:42 final size:41
Alignment explanation
Indices: 305432--305525 Score: 118
Period size: 40 Copynumber: 2.3 Consensus size: 41
305422 ATTTAACATT
* *
305432 TTGCGGCGTTTATACAAAAAAACGCCACTATTGATT-ACACTA
1 TTGCGGCGTTTAT--AAAAAAACACCACTATTGATTAAAACTA
* * *
305474 TTGTGGCGTTTGTTAAAAAACACCACTATTGATTAAAACTA
1 TTGCGGCGTTTATAAAAAAACACCACTATTGATTAAAACTA
305515 TTGCGGCGTTT
1 TTGCGGCGTTT
305526 TAAGAATAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
40 19 0.42
41 15 0.33
42 11 0.24
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (41 bp):
TTGCGGCGTTTATAAAAAAACACCACTATTGATTAAAACTA
Found at i:305500 original size:40 final size:41
Alignment explanation
Indices: 305448--305525 Score: 122
Period size: 40 Copynumber: 1.9 Consensus size: 41
305438 CGTTTATACA
* * *
305448 AAAAAACGCCACTATTGATT-ACACTATTGTGGCGTTTGTT
1 AAAAAACACCACTATTGATTAAAACTATTGCGGCGTTTGTT
305488 AAAAAACACCACTATTGATTAAAACTATTGCGGCGTTT
1 AAAAAACACCACTATTGATTAAAACTATTGCGGCGTTT
305526 TAAGAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 19 0.56
41 15 0.44
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (41 bp):
AAAAAACACCACTATTGATTAAAACTATTGCGGCGTTTGTT
Found at i:305577 original size:42 final size:42
Alignment explanation
Indices: 305551--305651 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
305541 CTATATGTGT
* *
305551 AATCTACTGCGGCGTTTGTGGTATAAACGCCGCTAATTTACC
1 AATCTACTGCGGCGTTTGTGGTATAAACGCCACTAATGTACC
* * *
305593 AATCTATTGTGGCGTTTGTGGTATAAACGCCACTAATTTACC
1 AATCTACTGCGGCGTTTGTGGTATAAACGCCACTAATGTACC
* * *
305635 ACTCTATTACGGCGTTT
1 AATCTACTGCGGCGTTT
305652 TTTAACAAAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.35
Consensus pattern (42 bp):
AATCTACTGCGGCGTTTGTGGTATAAACGCCACTAATGTACC
Found at i:307934 original size:2 final size:2
Alignment explanation
Indices: 307927--307955 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
307917 TGATCATGTG
307927 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
307956 TTCTTGATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:315690 original size:12 final size:12
Alignment explanation
Indices: 315644--315686 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
315634 TCTGCAAGCT
*
315644 TTTCCTTATTCC
1 TTTCCTTATTCA
315656 TTTCCTTATTCA
1 TTTCCTTATTCA
*
315668 TTTCCTTCTTCA
1 TTTCCTTATTCA
315680 TTTCCTT
1 TTTCCTT
315687 CTTCTTATTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTCCTTATTCA
Found at i:316925 original size:64 final size:64
Alignment explanation
Indices: 316857--316978 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
316847 ATTGTTCAAG
* * *
316857 GTGTATCAATGCACATGAAGTGTATCGATGCACTCC-TTTAAAATAAAAACATCGAATGTCATCA
1 GTGTATCAATGCACAAGAAGTGCATCGATGCAC-CCGCTTAAAATAAAAACATCGAATGTCATCA
* * * *
316921 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCGCTTAAAGTACAAACATCGAATG
1 GTGTATCAATGCACAAGAAGTGCATCGATGCACCCGCTTAAAATAAAAACATCGAATG
316979 GGATTTATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
63 2 0.04
64 48 0.96
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (64 bp):
GTGTATCAATGCACAAGAAGTGCATCGATGCACCCGCTTAAAATAAAAACATCGAATGTCATCA
Found at i:317740 original size:18 final size:18
Alignment explanation
Indices: 317717--317752 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
317707 AGGTATTATC
317717 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
317735 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
317753 TTCATAGTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:318740 original size:22 final size:20
Alignment explanation
Indices: 318715--318761 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
318705 GGGAAGTTTT
318715 GATACCAGTTGAGGAGGGTATC
1 GATACCAG--GAGGAGGGTATC
* *
318737 GATACCAGGGGGATGGTATC
1 GATACCAGGAGGAGGGTATC
318757 GATAC
1 GATAC
318762 TATTTTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 15 0.65
22 8 0.35
ACGTcount: A:0.28, C:0.15, G:0.36, T:0.21
Consensus pattern (20 bp):
GATACCAGGAGGAGGGTATC
Found at i:318761 original size:42 final size:42
Alignment explanation
Indices: 318662--318762 Score: 107
Period size: 42 Copynumber: 2.4 Consensus size: 42
318652 GTATTCCTTA
* * *
318662 AGGGTAGTATCGATACTCGTTGAGGAGTGTATCGATACTGAG
1 AGGGAAGTATCGATACTCGTTGAGGAGGGTATCGATACTCAG
* *
318704 AGGGAAGTTTTGATAC-CAGTTGAGGAGGGTATCGATAC-CAG
1 AGGGAAGTATCGATACTC-GTTGAGGAGGGTATCGATACTCAG
* *
318745 GGGGATGGTATCGATACT
1 AGGGA-AGTATCGATACT
318763 ATTTTTAAGA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
41 7 0.15
42 40 0.85
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.27
Consensus pattern (42 bp):
AGGGAAGTATCGATACTCGTTGAGGAGGGTATCGATACTCAG
Found at i:325597 original size:19 final size:20
Alignment explanation
Indices: 325568--325605 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
325558 AGAAATTTGT
325568 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
325588 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
325606 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:325648 original size:63 final size:62
Alignment explanation
Indices: 325573--325731 Score: 194
Period size: 63 Copynumber: 2.5 Consensus size: 62
325563 TTTGTTGAAG
* * * * *
325573 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATTGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
** **
325636 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
325699 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
325732 GCCTCCATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
63 79 0.94
64 5 0.06
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.27
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:327551 original size:149 final size:148
Alignment explanation
Indices: 327238--327540 Score: 489
Period size: 149 Copynumber: 2.0 Consensus size: 148
327228 GAGTCGAGGG
* * * * * *
327238 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* * *
327303 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGATATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
327368 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
* * *
327386 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACATAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
327451 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
327516 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGCAAT
327535 TCTACG
1 TCTACG
327541 TGGCACTTCG
Statistics
Matches: 142, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
148 48 0.34
149 94 0.66
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAAT
Found at i:330947 original size:19 final size:20
Alignment explanation
Indices: 330918--330955 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
330908 AGAAATTTGT
330918 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
330938 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
330956 TAATTTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:330998 original size:63 final size:62
Alignment explanation
Indices: 330923--331081 Score: 203
Period size: 63 Copynumber: 2.5 Consensus size: 62
330913 TTTGTTGAAG
* * * *
330923 GTGCATCGATGCATATGAAGTGCATCGATGCATTAAT-TTAAATACAAACATCGAATGTCGTCA
1 GTGCATCGATGCATA-GGAGTGCATCGATGCATTAATAATAAA-ACAAACATCGAATGCCCTCA
** **
330986 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTCTAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
331049 GTGCATCGATGCATCAGGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AGGAGTGCATCGATGCAT
331082 GCCTCAATTA
Statistics
Matches: 85, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
63 80 0.94
64 5 0.06
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCATAGGAGTGCATCGATGCATTAATAATAAAACAAACATCGAATGCCCTCA
Found at i:332857 original size:149 final size:148
Alignment explanation
Indices: 332588--332890 Score: 480
Period size: 149 Copynumber: 2.0 Consensus size: 148
332578 GAGTCGAGGG
* * * * * *
332588 TCTACGCGGTCCTTCGAGACATATGTATATTCTTTGGAACATTTATGAGGTCTTTGAGGCACATA
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
* *
332653 CTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
332718 ATGGCACTACGGTACAAT
131 ATGGCACTACGGTACAAT
** * *
332736 TCTACGCGGTCCTTTTAGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTATGAAGTCTT-TAAGACACAT
332801 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
332866 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTACAAT
332885 TCTACG
1 TCTACG
332891 TGGCACTTCG
Statistics
Matches: 141, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
148 46 0.33
149 95 0.67
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGAGACATATATATATTCTGTGGAACATGTATGAAGTCTTTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTACAAT
Found at i:332902 original size:23 final size:23
Alignment explanation
Indices: 332868--332913 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
332858 CATTATTATA
*
332868 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
332891 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
332914 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:334068 original size:22 final size:22
Alignment explanation
Indices: 334041--334114 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
334031 CTTAAGGGTA
334041 GTATCGATACCCGTTGAGGAGG
1 GTATCGATACCCGTTGAGGAGG
*
334063 GTATCGATA--C--TGAGAGAGAA
1 GTATCGATACCCGTTGAG-GAG-G
* *
334083 GTATCGATATCAGTTGAGGAGG
1 GTATCGATACCCGTTGAGGAGG
*
334105 ATATCGATAC
1 GTATCGATAC
334115 TGAAAGGATA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
18 4 0.10
19 3 0.07
20 10 0.24
22 17 0.41
23 3 0.07
24 4 0.10
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (22 bp):
GTATCGATACCCGTTGAGGAGG
Found at i:334087 original size:42 final size:42
Alignment explanation
Indices: 334034--334154 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 42
334024 TGTATTTCTT
* * *
334034 AAGGGTAGTATCGATACCCGTTGAGGAGGGTATCGATACTGA
1 AAGGATAGTATCGATACCAGTTGAGGAGGATATCGATACTGA
* *
334076 GAGAGA-AGTATCGATATCAGTTGAGGAGGATATCGATACTGA
1 AAG-GATAGTATCGATACCAGTTGAGGAGGATATCGATACTGA
* *
334118 AAGGATAGTATCGATACCAG--GGGGATGATATCGATAC
1 AAGGATAGTATCGATACCAGTTGAGGAGGATATCGATAC
334155 CATTTTTAAT
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
40 15 0.22
41 2 0.03
42 50 0.74
43 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.23
Consensus pattern (42 bp):
AAGGATAGTATCGATACCAGTTGAGGAGGATATCGATACTGA
Found at i:334088 original size:20 final size:20
Alignment explanation
Indices: 334063--334134 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
334053 GTTGAGGAGG
334063 GTATCGATACTGAGAGAGAA
1 GTATCGATACTGAGAGAGAA
*
334083 GTATCGATATCAGTTGAG-GAGGA
1 GTATCGATA-C---TGAGAGAGAA
*
334106 -TATCGATACTGAAAG-GATA
1 GTATCGATACTGAGAGAGA-A
334125 GTATCGATAC
1 GTATCGATAC
334135 CAGGGGGATG
Statistics
Matches: 42, Mismatches: 3, Indels: 14
0.71 0.05 0.24
Matches are distributed among these distances:
18 4 0.10
19 2 0.05
20 18 0.43
21 2 0.05
22 8 0.19
23 4 0.10
24 4 0.10
ACGTcount: A:0.36, C:0.11, G:0.28, T:0.25
Consensus pattern (20 bp):
GTATCGATACTGAGAGAGAA
Found at i:335886 original size:20 final size:20
Alignment explanation
Indices: 335833--335886 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
335823 AAGTATAGCT
*
335833 TAAACATAAAATCCATAAAATA
1 TAAACA-AAAAACCA-AAAATA
* *
335855 TAAACAATAAACCAAAAATT
1 TAAACAAAAAACCAAAAATA
*
335875 TAAATAAAAAAC
1 TAAACAAAAAAC
335887 AATTAAAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 15 0.56
21 6 0.22
22 6 0.22
ACGTcount: A:0.67, C:0.13, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAACAAAAAACCAAAAATA
Found at i:336324 original size:17 final size:17
Alignment explanation
Indices: 336302--336364 Score: 65
Period size: 17 Copynumber: 3.7 Consensus size: 17
336292 GATGACTATA
336302 AAACATCTGATATTTGT
1 AAACATCTGATATTTGT
*
336319 AAACATTTGATAGTTT-T
1 AAACATCTGATA-TTTGT
* * *
336336 AATCATATGATATATGT
1 AAACATCTGATATTTGT
*
336353 AAATATCTGATA
1 AAACATCTGATA
336365 ACTGTAAATA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
16 2 0.05
17 32 0.86
18 3 0.08
ACGTcount: A:0.40, C:0.08, G:0.11, T:0.41
Consensus pattern (17 bp):
AAACATCTGATATTTGT
Found at i:336370 original size:17 final size:17
Alignment explanation
Indices: 336350--336407 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
336340 ATATGATATA
336350 TGTAAATATCTGATAAC
1 TGTAAATATCTGATAAC
*
336367 TGTAAATATATGATAA-
1 TGTAAATATCTGATAAC
* *
336383 TGGTGTAATGTCTGATAAC
1 T-GT-AAATATCTGATAAC
336402 TGTAAA
1 TGTAAA
336408 CATTTAGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
16 1 0.03
17 19 0.58
18 12 0.36
19 1 0.03
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (17 bp):
TGTAAATATCTGATAAC
Found at i:336390 original size:19 final size:17
Alignment explanation
Indices: 336340--336382 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
336330 AGTTTTAATC
336340 ATATGATATA-TGTAAAT
1 ATATGATA-ACTGTAAAT
*
336357 ATCTGATAACTGTAAAT
1 ATATGATAACTGTAAAT
336374 ATATGATAA
1 ATATGATAA
336383 TGGTGTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.47, C:0.05, G:0.12, T:0.37
Consensus pattern (17 bp):
ATATGATAACTGTAAAT
Found at i:338177 original size:2 final size:2
Alignment explanation
Indices: 338170--338216 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
338160 TAGTCGAACC
338170 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
338212 AT AT A
1 AT AT A
338217 GTCTTACGCT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:340295 original size:2 final size:2
Alignment explanation
Indices: 340288--340362 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
340278 GTCCCTCTCC
340288 AT AT AT AT AT AT AT AT AT AT AT AT -T 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
340329 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
340363 GCATAACAAC
Statistics
Matches: 72, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 71 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:341304 original size:17 final size:16
Alignment explanation
Indices: 341273--341307 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
341263 AAATTGAAAA
341273 AATATAATATATATAT
1 AATATAATATATATAT
*
341289 AATATAAGTTTATATAT
1 AATATAA-TATATATAT
341306 AA
1 AA
341308 ACTATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AATATAATATATATAT
Found at i:341333 original size:20 final size:19
Alignment explanation
Indices: 341298--341354 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
341288 TAATATAAGT
* *
341298 TTATATATAAACTATATTTA
1 TTAT-TATAAATTATATATA
341318 -TATTATAAATTATATA-A
1 TTATTATAAATTATATATA
*
341335 TTATTATAAGTTATATATA
1 TTATTATAAATTATATATA
341354 T
1 T
341355 AAATTATGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.03
18 26 0.81
19 5 0.16
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.51
Consensus pattern (19 bp):
TTATTATAAATTATATATA
Found at i:341394 original size:13 final size:13
Alignment explanation
Indices: 341371--341396 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
341361 TGTTTATATG
341371 AACTATATATGTA
1 AACTATATATGTA
341384 AACTATATATGTA
1 AACTATATATGTA
341397 TAAACTATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
AACTATATATGTA
Found at i:341557 original size:17 final size:17
Alignment explanation
Indices: 341524--341557 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
341514 TTGAGAAATT
*
341524 TTGAGAATATAGGGAAA
1 TTGAGAATATAGAGAAA
*
341541 TTGAGAATTTAGAGAAA
1 TTGAGAATATAGAGAAA
341558 AATTGGAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.26, T:0.26
Consensus pattern (17 bp):
TTGAGAATATAGAGAAA
Found at i:341801 original size:2 final size:2
Alignment explanation
Indices: 341794--341926 Score: 95
Period size: 2 Copynumber: 68.5 Consensus size: 2
341784 TTAATTTTCC
341794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* * *
341837 AT AGT TT AT AA AT -T AT A- AT TT AT AT -T A- AT AT AGT AT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * *
341877 AT GT AT GT AT A- ACT A- AT AT A- AGT A- AT CT AT AG AT -T AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT
341916 AT AT AT AT AT A
1 AT AT AT AT AT A
341927 GTTTATAGAA
Statistics
Matches: 103, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
1 9 0.09
2 87 0.84
3 7 0.07
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (2 bp):
AT
Found at i:342091 original size:15 final size:15
Alignment explanation
Indices: 342066--342117 Score: 77
Period size: 15 Copynumber: 3.4 Consensus size: 15
342056 ATAAATCATG
342066 TATAGTATATATAAAC
1 TATA-TATATATAAAC
*
342082 TATATATATATAACC
1 TATATATATATAAAC
*
342097 TATATATATAAAAAC
1 TATATATATATAAAC
342112 TATATA
1 TATATA
342118 AAGTAAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
15 29 0.88
16 4 0.12
ACGTcount: A:0.52, C:0.08, G:0.02, T:0.38
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:342328 original size:7 final size:7
Alignment explanation
Indices: 342318--342385 Score: 75
Period size: 7 Copynumber: 9.7 Consensus size: 7
342308 TAGTTTATAG
*
342318 AAACCCT
1 AAACCAT
*
342325 AAACCCT
1 AAACCAT
*
342332 AAATCAT
1 AAACCAT
342339 AAACCAT
1 AAACCAT
342346 AAACCAT
1 AAACCAT
*
342353 AAA-TATT
1 AAACCA-T
342360 AAACCAT
1 AAACCAT
*
342367 GAACCAT
1 AAACCAT
342374 AAACCAT
1 AAACCAT
342381 AAACC
1 AAACC
342386 CTAATATAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
6 1 0.02
7 50 0.96
8 1 0.02
ACGTcount: A:0.53, C:0.28, G:0.01, T:0.18
Consensus pattern (7 bp):
AAACCAT
Found at i:342348 original size:21 final size:21
Alignment explanation
Indices: 342318--342385 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
342308 TAGTTTATAG
* *
342318 AAACCCTAAACCCTAAATCAT
1 AAACCATAAACCATAAATCAT
342339 AAACCATAAACCATAAAT-ATT
1 AAACCATAAACCATAAATCA-T
* *
342360 AAACCATGAACCATAAACCAT
1 AAACCATAAACCATAAATCAT
342381 AAACC
1 AAACC
342386 CTAATATAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.02
21 39 0.95
22 1 0.02
ACGTcount: A:0.53, C:0.28, G:0.01, T:0.18
Consensus pattern (21 bp):
AAACCATAAACCATAAATCAT
Found at i:342363 original size:125 final size:125
Alignment explanation
Indices: 342145--342378 Score: 332
Period size: 125 Copynumber: 1.9 Consensus size: 125
342135 AGTTTATAGA
*
342145 AACACTATGCATAAACTATATAAAGTAATAAAGTATATAGGTTTATAGAAACCCTAAACCCTAAA
1 AACACTATGCATAAACTATATAAAGTAATAAAATATATAGGTTTATAGAAACCCTAAACCCTAAA
** * *
342210 CTATAAATCCTAAACTTTAACCCGTAAA-CACTAAACCATAAACCTTAATGTAAATGGAAT
66 CTATAAATCCTAAACCATAAACAGTAAACCA-TAAACCATAAACCTTAATGTAAATGGAAT
342270 AACACTAATGCATAAACTATATAAAGTAATAAAATATATA-GTTTATAGAAACCCTAAACCCTAA
1 AACACT-ATGCATAAACTATATAAAGTAATAAAATATATAGGTTTATAGAAACCCTAAACCCTAA
* * *
342334 A-TCATAAA-CCATAAACCATAAATATTAAACCATGAACCATAAACC
65 ACT-ATAAATCC-TAAACCATAAACAGTAAACCATAAACCATAAACC
342379 ATAAACCCTA
Statistics
Matches: 97, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
124 3 0.03
125 60 0.62
126 34 0.35
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (125 bp):
AACACTATGCATAAACTATATAAAGTAATAAAATATATAGGTTTATAGAAACCCTAAACCCTAAA
CTATAAATCCTAAACCATAAACAGTAAACCATAAACCATAAACCTTAATGTAAATGGAAT
Found at i:343454 original size:13 final size:14
Alignment explanation
Indices: 343438--343473 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
343428 ATTAATATAG
343438 TATATA-TATAAAC
1 TATATAGTATAAAC
343451 TATATATGTATAAAC
1 TATATA-GTATAAAC
343466 TATATAGT
1 TATATAGT
343474 TTATAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.29
14 2 0.10
15 13 0.62
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.42
Consensus pattern (14 bp):
TATATAGTATAAAC
Found at i:343456 original size:15 final size:15
Alignment explanation
Indices: 343411--343507 Score: 65
Period size: 16 Copynumber: 6.3 Consensus size: 15
343401 GTATATAGTT
*
343411 TATAAACTATAATTTA
1 TATAAACTAT-ATATA
343427 TATTAATA-TAGTATATA
1 TA-TAA-ACTA-TATATA
*
343444 TATAAACTATATATG
1 TATAAACTATATATA
*
343459 TATAAACTATATAGTT
1 TATAAACTATATA-TA
* *
343475 TATAAATTATAATTTA
1 TATAAACTAT-ATATA
*
343491 TATTAA-TATA-ATA
1 TATAAACTATATATA
343504 TATA
1 TATA
343508 TCTGTATGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
13 5 0.08
14 1 0.02
15 22 0.33
16 23 0.35
17 13 0.20
18 2 0.03
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (15 bp):
TATAAACTATATATA
Found at i:343508 original size:15 final size:15
Alignment explanation
Indices: 343418--343508 Score: 51
Period size: 15 Copynumber: 5.8 Consensus size: 15
343408 GTTTATAAAC
*
343418 TATAATTTATATTAA
1 TATAATATATATTAA
*
343433 TATAGTATATATATAA
1 TATAATATATAT-TAA
* *
343449 -ACTATATATGTATAAA
1 TA-TA-ATATATATTAA
* *
343465 CTAT-ATAGTTTATAAA
1 -TATAATA-TATATTAA
*
343481 TTATAATTTATATTAA
1 -TATAATATATATTAA
343497 TATAATATATAT
1 TATAATATATAT
343509 CTGTATGTAT
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
15 25 0.43
16 23 0.40
17 9 0.16
18 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.47
Consensus pattern (15 bp):
TATAATATATATTAA
Found at i:343731 original size:7 final size:7
Alignment explanation
Indices: 343721--343778 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
343711 TAGTGTATAG
343721 AAACCCT
1 AAACCCT
*
343728 AAACCTT
1 AAACCCT
* *
343735 AAATCAT
1 AAACCCT
343742 AAACCCT
1 AAACCCT
**
343749 AAACTAT
1 AAACCCT
*
343756 AAACACT
1 AAACCCT
343763 AAACCCT
1 AAACCCT
*
343770 AAATCCT
1 AAACCCT
343777 AA
1 AA
343779 TATAAATGAA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 40 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (7 bp):
AAACCCT
Found at i:343747 original size:21 final size:21
Alignment explanation
Indices: 343721--343772 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
343711 TAGTGTATAG
343721 AAACCCTAAACCT-TAAATCA-T
1 AAACCCTAAA-CTATAAA-CACT
343742 AAACCCTAAACTATAAACACT
1 AAACCCTAAACTATAAACACT
343763 AAACCCTAAA
1 AAACCCTAAA
343773 TCCTAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.14
21 25 0.86
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (21 bp):
AAACCCTAAACTATAAACACT
Found at i:344174 original size:17 final size:18
Alignment explanation
Indices: 344127--344185 Score: 77
Period size: 17 Copynumber: 3.3 Consensus size: 18
344117 ATTTTATATA
*
344127 ATAT-GTATGTATAAACCAT
1 ATATAGTATATATAAA-C-T
344146 ATATAGTATATATAAACT
1 ATATAGTATATATAAACT
344164 ATATA-TATATATAAACT
1 ATATAGTATATATAAACT
344181 ATATA
1 ATATA
344186 AAGTATATTA
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
17 17 0.45
18 6 0.16
19 5 0.13
20 10 0.26
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (18 bp):
ATATAGTATATATAAACT
Found at i:344271 original size:14 final size:14
Alignment explanation
Indices: 344252--344282 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
344242 TAGTTTATAG
*
344252 AAATCTTAAACCTT
1 AAATCTTAAACCCT
344266 AAATCTTAAACCCT
1 AAATCTTAAACCCT
344280 AAA
1 AAA
344283 CCATAAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATCTTAAACCCT
Found at i:344295 original size:34 final size:35
Alignment explanation
Indices: 344252--344323 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 35
344242 TAGTTTATAG
* * *
344252 AAATCTTAAACCTTAAATC-TTAAACCCTAAACCAT
1 AAATCTTAAACCATAAA-CACTAAACACTAAACCAT
344287 AAAT-TTAAACCATAAACACTAAACACTAAACCAT
1 AAATCTTAAACCATAAACACTAAACACTAAACCAT
344321 AAA
1 AAA
344324 CCCTAATATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 1 0.03
34 28 0.85
35 4 0.12
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.24
Consensus pattern (35 bp):
AAATCTTAAACCATAAACACTAAACACTAAACCAT
Found at i:344329 original size:14 final size:14
Alignment explanation
Indices: 344258--344325 Score: 50
Period size: 14 Copynumber: 4.9 Consensus size: 14
344248 ATAGAAATCT
* * *
344258 TAAACCTTAAATCT
1 TAAACCCTAAACCA
344272 TAAACCCTAAACCA
1 TAAACCCTAAACCA
**
344286 TAAA-TTTAAACCA
1 TAAACCCTAAACCA
*
344299 TAAACACTAAA-CA
1 TAAACCCTAAACCA
*
344312 CTAAACCATAAACC
1 -TAAACCCTAAACC
344326 CTAATATAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
13 13 0.31
14 28 0.67
15 1 0.02
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACCA
Found at i:344823 original size:16 final size:16
Alignment explanation
Indices: 344802--344856 Score: 101
Period size: 16 Copynumber: 3.4 Consensus size: 16
344792 CGGATCATTT
*
344802 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
344818 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
344834 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
344850 ACAGGTC
1 ACAGGTC
344857 GGGTAATACC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.38, C:0.15, G:0.29, T:0.18
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:355202 original size:21 final size:21
Alignment explanation
Indices: 355178--355233 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
355168 AAAATAAAAA
* **
355178 TATAATAATTATTATTATTAT
1 TATAATAATTATAACAATTAT
*
355199 TATAATAAATATAACAATTAT
1 TATAATAATTATAACAATTAT
*
355220 TATAATAATAATAA
1 TATAATAATTATAA
355234 TAAACGGGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TATAATAATTATAACAATTAT
Found at i:355209 original size:30 final size:30
Alignment explanation
Indices: 355163--355237 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
355153 TAATATTTAT
* *
355163 TAATAAAAATAA-AAATATAATAATTATTA
1 TAATAATAATAATAAATATAACAATTATTA
* * *
355192 TTATTATTATAATAAATATAACAATTATTA
1 TAATAATAATAATAAATATAACAATTATTA
355222 TAATAATAATAATAAA
1 TAATAATAATAATAAA
355238 CGGGAAAAAA
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (30 bp):
TAATAATAATAATAAATATAACAATTATTA
Found at i:355781 original size:139 final size:139
Alignment explanation
Indices: 355453--355794 Score: 433
Period size: 138 Copynumber: 2.5 Consensus size: 139
355443 CAAAAAATTT
* * *
355453 GAACAAGTTCTTATTATTATGAACTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTATGAA-AT
1 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
* * * * * * *
355517 CCTTCTCGAAATGTTAATCCTCAAAAGAGGGGTTGTTGATTCAGCTTCATATGTGATGAATTTAA
66 CCTTCTCGAAATGTTAATCCTCAAAAGAGGGCTTGTTCATTCAACTCCATAGGAGATGAATTCAA
*
355582 GACAAGGTT
131 GACAAGGTC
* *
355591 GAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTATTCAGATGAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
* * * *
355656 CC-TCT-GAAAATGTTTATCCTCAAGAGAGGTTCTTCTTTCATTCAACTCCATAGGAGATGAA-T
66 CCTTCTCG-AAATGTTAATCCTCAAAAGAGG-GCTT-GTTCATTCAACTCCATAGGAGATGAATT
*
355718 CAAG-CTAATGTC
128 CAAGAC-AAGGTC
* *
355730 GAGCAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACTT
1 GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
355795 TATCGGAAAT
Statistics
Matches: 177, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
137 1 0.01
138 82 0.46
139 74 0.42
140 20 0.11
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.39
Consensus pattern (139 bp):
GAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTT
CCTTCTCGAAATGTTAATCCTCAAAAGAGGGCTTGTTCATTCAACTCCATAGGAGATGAATTCAA
GACAAGGTC
Found at i:356078 original size:112 final size:112
Alignment explanation
Indices: 355857--356140 Score: 383
Period size: 112 Copynumber: 2.5 Consensus size: 112
355847 AGGTTGAACA
* * * * * *
355857 AGTTCTTCTCATTATGAACTTCTT-TTGGAAAAGTTGATCCATCGAGTGATGAATTCAATCAAAA
1 AGTTCTTCTCATTATGAAC-TCTTCCTGGTAATGTTGATCCATTGAGTAATGAATTCAAGCAAAA
* *
355921 GGTTTGAACAAATTCTTCTCATTATAAATTTCTTCTTCCTATCAGATG
65 GGTTTAAACAAATTCTTCTCATTATAAACTTCTTCTTCCTATCAGATG
*
355969 AGTTCTTCTCATTATGAACTCTTCCTGGTAATGTTGATCCATTGAGTAATGGATTCAAGCAAAAG
1 AGTTCTTCTCATTATGAACTCTTCCTGGTAATGTTGATCCATTGAGTAATGAATTCAAGCAAAAG
* * * *
356034 G-TTAAACAAGTTCTTCTCATTATGAACTTCTTTTTCCTCCTCAGATG
66 GTTTAAACAAATTCTTCTCATTATAAACTTCTTCTTCCT-ATCAGATG
* * * *
356081 AGTTCTTCTCATTATGAAATCTTCCTGGTAATGTTAATCCATTGAGTGACGAATTCAAGC
1 AGTTCTTCTCATTATGAACTCTTCCTGGTAATGTTGATCCATTGAGTAATGAATTCAAGC
356141 CTTTGCTAAA
Statistics
Matches: 152, Mismatches: 18, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
111 36 0.24
112 116 0.76
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (112 bp):
AGTTCTTCTCATTATGAACTCTTCCTGGTAATGTTGATCCATTGAGTAATGAATTCAAGCAAAAG
GTTTAAACAAATTCTTCTCATTATAAACTTCTTCTTCCTATCAGATG
Found at i:357252 original size:21 final size:21
Alignment explanation
Indices: 357223--357263 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
357213 TTTATGTGAA
*
357223 AAAATAAATTGAATTTCAAAC
1 AAAAGAAATTGAATTTCAAAC
357244 AAAAGAAATTGAATTTCAAA
1 AAAAGAAATTGAATTTCAAA
357264 AAGATAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.59, C:0.07, G:0.07, T:0.27
Consensus pattern (21 bp):
AAAAGAAATTGAATTTCAAAC
Found at i:357619 original size:2 final size:2
Alignment explanation
Indices: 357612--357656 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
357602 CCTCATTTTC
357612 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
357654 TA T
1 TA T
357657 TTCATTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:357670 original size:9 final size:9
Alignment explanation
Indices: 357656--357694 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
357646 TATATATATA
357656 TTTCATTTT
1 TTTCATTTT
357665 TTTCATTTT
1 TTTCATTTT
*
357674 TTTTATTTT
1 TTTCATTTT
*
357683 TCATCATTTT
1 T-TTCATTTT
357693 TT
1 TT
357695 CTTTTTCAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 18 0.72
10 7 0.28
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTCATTTT
Found at i:357684 original size:16 final size:17
Alignment explanation
Indices: 357663--357702 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
357653 ATATTTCATT
*
357663 TTTTTCAT-TTTTTTTA
1 TTTTTCATCATTTTTTA
*
357679 TTTTTCATCATTTTTTC
1 TTTTTCATCATTTTTTA
357696 TTTTTCA
1 TTTTTCA
357703 AACATAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCATCATTTTTTA
Found at i:364929 original size:14 final size:16
Alignment explanation
Indices: 364912--364943 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
364902 ATTATTTTTT
364912 TGAAT-TTTAT-TTAA
1 TGAATGTTTATCTTAA
364926 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
364942 TG
1 TG
364944 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:368872 original size:2 final size:2
Alignment explanation
Indices: 368865--368896 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
368855 TAAGAAAATC
368865 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
368897 AATAAGATAT
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):
TA
Found at i:369250 original size:3 final size:3
Alignment explanation
Indices: 369242--369271 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
369232 TACATGACTA
369242 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
369272 TAAATATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:370648 original size:3 final size:3
Alignment explanation
Indices: 370640--370750 Score: 57
Period size: 3 Copynumber: 37.0 Consensus size: 3
370630 GCCTGTTTTG
* * *
370640 TAA TAA TAA TATT TAT TAA TAA TAA TAA AAA T-A TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * * *
370685 TTA TTA TTA TTA TAA TAA -ATA TAA CAA TTA TTA TAA TAA -ATA TAA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA
* * *
370730 CAA TTA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
370751 ACGGGCAAAA
Statistics
Matches: 88, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
2 4 0.05
3 80 0.91
4 4 0.05
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:370681 original size:33 final size:33
Alignment explanation
Indices: 370640--370708 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
370630 GCCTGTTTTG
*
370640 TAATAATAATATTTATTAATAATAATAA-AAATA
1 TAATAATAATAATTATT-ATAATAATAATAAATA
* *
370673 TAATAATAATAATTATTATTATTATAATAAATA
1 TAATAATAATAATTATTATAATAATAATAAATA
370706 TAA
1 TAA
370709 CAATTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
32 8 0.25
33 24 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (33 bp):
TAATAATAATAATTATTATAATAATAATAAATA
Found at i:370701 original size:21 final size:21
Alignment explanation
Indices: 370690--370744 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
370680 AATAATTATT
370690 ATTATTATAATAAATATAACA
1 ATTATTATAATAAATATAACA
370711 ATTATTATAATAAATATAACA
1 ATTATTATAATAAATATAACA
370732 ATTATTATAATAA
1 ATTATTATAATAA
370745 TAATAAACGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTATTATAATAAATATAACA
Found at i:370701 original size:24 final size:24
Alignment explanation
Indices: 370672--370750 Score: 81
Period size: 24 Copynumber: 3.3 Consensus size: 24
370662 TAATAAAAAT
*
370672 ATAATAATAATAATTATTATTATT
1 ATAATAATAATAATTATTATTATA
**
370696 ATAATAA-ATATAACAATTATTATA
1 ATAATAATA-ATAATTATTATTATA
* *
370720 ATAA-ATATAACAATTATTATAATA
1 ATAATA-ATAATAATTATTATTATA
370744 ATAATAA
1 ATAATAA
370751 ACGGGCAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
23 2 0.05
24 40 0.91
25 2 0.05
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (24 bp):
ATAATAATAATAATTATTATTATA
Found at i:370750 original size:21 final size:21
Alignment explanation
Indices: 370640--370750 Score: 106
Period size: 21 Copynumber: 5.4 Consensus size: 21
370630 GCCTGTTTTG
* *
370640 TAATAATAATATTTA-T-TAA
1 TAATAATAACAATTATTATAA
* *
370659 TAATAATAA-AAATATAATAA
1 TAATAATAACAATTATTATAA
* **
370679 TAATAATTATTATTATTATAA
1 TAATAATAACAATTATTATAA
370700 TAA-ATATAACAATTATTATAA
1 TAATA-ATAACAATTATTATAA
370721 TAA-ATATAACAATTATTATAA
1 TAATA-ATAACAATTATTATAA
370742 TAATAATAA
1 TAATAATAA
370751 ACGGGCAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
18 3 0.04
19 9 0.12
20 12 0.16
21 52 0.68
22 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATAATAACAATTATTATAA
Found at i:373708 original size:20 final size:20
Alignment explanation
Indices: 373656--373709 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
373646 AACTTAATAT
*
373656 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
373678 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
373698 TATTATTTTTAT
1 TATTATTTTTAT
373710 AATTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:373801 original size:21 final size:21
Alignment explanation
Indices: 373761--373807 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
373751 AAATAAAAAT
*
373761 TTTA-TAAATTATATTAATTA
1 TTTATTAAATTATAGTAATTA
373781 TTTATTAAATTAATAGT-ATTA
1 TTTATTAAATT-ATAGTAATTA
373802 TATTAT
1 T-TTAT
373808 ATTTTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 4 0.17
21 11 0.48
22 8 0.35
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTATTAAATTATAGTAATTA
Found at i:373929 original size:53 final size:53
Alignment explanation
Indices: 373800--373902 Score: 138
Period size: 53 Copynumber: 2.0 Consensus size: 53
373790 TTAATAGTAT
* * * * *
373800 TATATTATAT-TTTAAAAATAATAATTAGTATATTTTAAATATCTTTATTAAA
1 TATATTATATAATTAAAAATATTAATAAATATATTTTAAATATCTTTAATAAA
*
373852 TATATTATATAATTAGAAATATTAATAAATATATTTTAAATAT-TTTAATAA
1 TATATTATATAATTAAAAATATTAATAAATATATTTTAAATATCTTTAATAA
373903 GTAATATTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
52 17 0.39
53 27 0.61
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.49
Consensus pattern (53 bp):
TATATTATATAATTAAAAATATTAATAAATATATTTTAAATATCTTTAATAAA
Found at i:379347 original size:23 final size:21
Alignment explanation
Indices: 379299--379347 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
379289 TTTTCAGTAC
379299 TTTA-GTTTTATTCCTTTAAT
1 TTTATGTTTTATTCCTTTAAT
*
379319 TATTATGTTTTATTTCCTCTTTAT
1 T-TTATGTTTTA-TTCCT-TTAAT
379343 TTTAT
1 TTTAT
379348 TTTAGTCCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 1 0.04
21 3 0.12
22 6 0.25
23 9 0.38
24 5 0.21
ACGTcount: A:0.18, C:0.10, G:0.04, T:0.67
Consensus pattern (21 bp):
TTTATGTTTTATTCCTTTAAT
Found at i:379462 original size:16 final size:16
Alignment explanation
Indices: 379443--379488 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
379433 TTATTTATGT
379443 ATGTATATATTATATC
1 ATGTATATATTATATC
*
379459 ATGT-TATA-GATATAC
1 ATGTATATATTATAT-C
379474 ATGTATATATT-TATC
1 ATGTATATATTATATC
379489 TAATATTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
14 4 0.16
15 10 0.40
16 11 0.44
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.48
Consensus pattern (16 bp):
ATGTATATATTATATC
Found at i:383290 original size:14 final size:14
Alignment explanation
Indices: 383271--383299 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
383261 ATCAAAGCAA
383271 AGCAAAAAAAAAAG
1 AGCAAAAAAAAAAG
383285 AGCAAAAAAAAAAG
1 AGCAAAAAAAAAAG
383299 A
1 A
383300 AAAAAGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (14 bp):
AGCAAAAAAAAAAG
Found at i:383304 original size:21 final size:20
Alignment explanation
Indices: 383274--383322 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
383264 AAAGCAAAGC
*
383274 AAAA-AAAAAAGAGCAAAAAA
1 AAAAGAAAAAAGA-AAAAAAA
383294 AAAAGAAAAAAGAAAAAAAA
1 AAAAGAAAAAAGAAAAAAAA
383314 AATAAGAAA
1 AA-AAGAAA
383323 CGAATCAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAAAGAAAAAAAA
Done.