Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008054.1 Hibiscus syriacus cultivar Beakdansim tig00110549_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: 738886
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
File 2 of 3
Found at i:376662 original size:15 final size:15
Alignment explanation
Indices: 376642--376750 Score: 80
Period size: 15 Copynumber: 7.3 Consensus size: 15
376632 GGAGGCTGTG
376642 CCTTCTTCTCTTCCT
1 CCTTCTTCTCTTCCT
* *
376657 CCTTCTTCCCTTCTT
1 CCTTCTTCTCTTCCT
376672 CCTTCTTCTC-TCC-
1 CCTTCTTCTCTTCCT
*
376685 CCTTCTTTTCTCTCCT
1 CCTTCTTCTCT-TCCT
* *
376701 CTTTCTTTTC-TCCTT
1 CCTTCTTCTCTTCC-T
* *
376716 CCTTCTTTTCTCCCTT
1 CCTTCTTCTCTTCC-T
* * *
376732 CTTTCTTCGCTTCTT
1 CCTTCTTCTCTTCCT
376747 CCTT
1 CCTT
376751 TTTCGGCTCC
Statistics
Matches: 75, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
13 9 0.12
14 5 0.07
15 39 0.52
16 22 0.29
ACGTcount: A:0.00, C:0.43, G:0.01, T:0.56
Consensus pattern (15 bp):
CCTTCTTCTCTTCCT
Found at i:376707 original size:44 final size:42
Alignment explanation
Indices: 376642--376739 Score: 117
Period size: 44 Copynumber: 2.3 Consensus size: 42
376632 GGAGGCTGTG
* *
376642 CCTTCTTCTCTTCCTCCTTCTTCCCTTCTTCCTTCTTCTCTCC
1 CCTTCTTTTCTTCCTCCTTCTTCCCTCCTTCCTTCTTCTCT-C
* ** *
376685 CCTTCTTTTCTCTCCTCTTTCTTTTCTCCTTCCTTCTTTTCTC
1 CCTTCTTTTCT-TCCTCCTTCTTCCCTCCTTCCTTCTTCTCTC
376728 CCTTC-TTTCTTC
1 CCTTCTTTTCTTC
376740 GCTTCTTCCT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 2 0.04
42 5 0.10
43 16 0.33
44 25 0.52
ACGTcount: A:0.00, C:0.44, G:0.00, T:0.56
Consensus pattern (42 bp):
CCTTCTTTTCTTCCTCCTTCTTCCCTCCTTCCTTCTTCTCTC
Found at i:376720 original size:31 final size:31
Alignment explanation
Indices: 376685--376769 Score: 95
Period size: 31 Copynumber: 2.8 Consensus size: 31
376675 TCTTCTCTCC
**
376685 CCTTCTTTTCTCTCCTCTTTCTTTTCTCCTT
1 CCTTCTTTTCTCTCCTCTTTCTTCGCTCCTT
*
376716 CCTTCTTTTCTC-CCTTCTTTCTTCGCTTCTT
1 CCTTCTTTTCTCTCC-TCTTTCTTCGCTCCTT
*
376747 CC-T-TTTTCGGCTCCTCTTTCTTC
1 CCTTCTTTTC-TCTCCTCTTTCTTC
376770 TCCGGTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
29 5 0.11
30 13 0.28
31 29 0.62
ACGTcount: A:0.00, C:0.39, G:0.04, T:0.58
Consensus pattern (31 bp):
CCTTCTTTTCTCTCCTCTTTCTTCGCTCCTT
Found at i:378479 original size:24 final size:24
Alignment explanation
Indices: 378447--378492 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
378437 TTCGTGAACA
*
378447 TTCGATTATATTCGTTTATGTTCG
1 TTCGATTATATTCATTTATGTTCG
* *
378471 TTCGGTTATGTTCATTTATGTT
1 TTCGATTATATTCATTTATGTT
378493 TAATCAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.15, C:0.11, G:0.17, T:0.57
Consensus pattern (24 bp):
TTCGATTATATTCATTTATGTTCG
Found at i:378960 original size:10 final size:10
Alignment explanation
Indices: 378945--379033 Score: 52
Period size: 10 Copynumber: 9.5 Consensus size: 10
378935 GTTTCCAACA
378945 TTTATGTTCG
1 TTTATGTTCG
378955 TTTATGTTCG
1 TTTATGTTCG
*
378965 TGTTCAT-TTATG
1 T-TT-ATGTT-CG
**
378977 TTCGTGTTCG
1 TTTATGTTCG
378987 TTTATGTTCG
1 TTTATGTTCG
378997 ----TGTTCG
1 TTTATGTTCG
379003 TTTATGTTCG
1 TTTATGTTCG
379013 ----TGTTCG
1 TTTATGTTCG
*
379019 TTTATATTCG
1 TTTATGTTCG
379029 TTTAT
1 TTTAT
379034 TTATTAAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 24
0.66 0.08 0.26
Matches are distributed among these distances:
6 12 0.20
10 37 0.62
11 7 0.12
12 4 0.07
ACGTcount: A:0.10, C:0.11, G:0.20, T:0.58
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:378974 original size:16 final size:16
Alignment explanation
Indices: 378949--379029 Score: 144
Period size: 16 Copynumber: 5.1 Consensus size: 16
378939 CCAACATTTA
378949 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
378965 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
378981 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
378997 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
379013 TGTTCGTTTATATTCG
1 TGTTCGTTTATGTTCG
379029 T
1 T
379030 TTATTTATTA
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 62 1.00
ACGTcount: A:0.09, C:0.12, G:0.22, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:379124 original size:16 final size:14
Alignment explanation
Indices: 379100--379138 Score: 60
Period size: 16 Copynumber: 2.6 Consensus size: 14
379090 AATAAATTTT
379100 TTTATTTATGTTCG
1 TTTATTTATGTTCG
379114 TGTTCATTTATGTTCG
1 T-TT-ATTTATGTTCG
379130 TTTATTTAT
1 TTTATTTAT
379139 TAAATGAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.30
15 4 0.17
16 12 0.52
ACGTcount: A:0.15, C:0.08, G:0.13, T:0.64
Consensus pattern (14 bp):
TTTATTTATGTTCG
Found at i:380928 original size:27 final size:26
Alignment explanation
Indices: 380898--381023 Score: 80
Period size: 27 Copynumber: 4.6 Consensus size: 26
380888 AATATTTAAA
380898 TATATTTATTAATATATAATATTATAT
1 TATATTTATTAATATATAATATTAT-T
*
380925 TATATTT-TTAATATTATAATAAAATAATCAAT
1 TATATTTATTAATA-TATAAT---AT--T-ATT
*
380957 TATATTGTAATAATATA-AGATATTATT
1 TATATT-TATTAATATATA-ATATTATT
* *
380984 TTTATTTAATAAATATATAATATT-TT
1 TATATTT-ATTAATATATAATATTATT
*
381010 TATATAT-TTAATAT
1 TATATTTATTAATAT
381024 TGATATAATA
Statistics
Matches: 78, Mismatches: 9, Indels: 27
0.68 0.08 0.24
Matches are distributed among these distances:
24 6 0.08
26 14 0.18
27 32 0.41
28 2 0.03
30 4 0.05
32 9 0.12
33 6 0.08
34 5 0.06
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (26 bp):
TATATTTATTAATATATAATATTATT
Found at i:381068 original size:23 final size:23
Alignment explanation
Indices: 381048--381092 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
381038 AATAATATTT
381048 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
381071 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
381093 AAATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:381414 original size:15 final size:15
Alignment explanation
Indices: 381388--381447 Score: 61
Period size: 15 Copynumber: 4.1 Consensus size: 15
381378 ATAATTCATT
381388 TTTCAG-AATTCAAA
1 TTTCAGTAATTCAAA
* *
381402 TTTCAATAATTC-AT
1 TTTCAGTAATTCAAA
381416 TTTACAGTAATTCAAA
1 TTT-CAGTAATTCAAA
* *
381432 TTCCAGTAATTTAAA
1 TTTCAGTAATTCAAA
381447 T
1 T
381448 AGATTCAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
14 9 0.24
15 25 0.68
16 3 0.08
ACGTcount: A:0.40, C:0.13, G:0.05, T:0.42
Consensus pattern (15 bp):
TTTCAGTAATTCAAA
Found at i:381430 original size:30 final size:29
Alignment explanation
Indices: 381378--381442 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
381368 TTCCGTAAAT
* *
381378 ATAATTCATTTTTCAGAATTCAAATTTCA
1 ATAATTCATTTTACAGAATTCAAATTCCA
381407 ATAATTCATTTTACAGTAATTCAAATTCCA
1 ATAATTCATTTTACAG-AATTCAAATTCCA
*
381437 GTAATT
1 ATAATT
381443 TAAATAGATT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (29 bp):
ATAATTCATTTTACAGAATTCAAATTCCA
Found at i:382772 original size:13 final size:13
Alignment explanation
Indices: 382744--382784 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
382734 AAAATTTAAA
*
382744 TTATTATATATTTT
1 TTATT-TATATATT
382758 TTATTTATATATT
1 TTATTTATATATT
382771 TTA-TTATATATT
1 TTATTTATATATT
382783 TT
1 TT
382785 TTATTAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 11 0.42
13 10 0.38
14 5 0.19
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTATTTATATATT
Found at i:382786 original size:14 final size:14
Alignment explanation
Indices: 382744--382790 Score: 78
Period size: 14 Copynumber: 3.4 Consensus size: 14
382734 AAAATTTAAA
382744 TTATTATATATTTT
1 TTATTATATATTTT
*
382758 TTATT-TATATATT
1 TTATTATATATTTT
382771 TTATTATATATTTT
1 TTATTATATATTTT
382785 TTATTA
1 TTATTA
382791 AAAATTTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 12 0.40
14 18 0.60
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TTATTATATATTTT
Found at i:382804 original size:27 final size:27
Alignment explanation
Indices: 382744--382797 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
382734 AAAATTTAAA
* *
382744 TTATTATATATTTTTTATTTATATATT
1 TTATTATATATTTTTTATTTAAAAATT
382771 TTATTATATATTTTTTA-TTAAAAATT
1 TTATTATATATTTTTTATTTAAAAATT
382797 T
1 T
382798 ATTTTATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 8 0.32
27 17 0.68
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTATTATATATTTTTTATTTAAAAATT
Found at i:383516 original size:12 final size:12
Alignment explanation
Indices: 383499--383531 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
383489 TTTTAATAGT
383499 TATATATTTATA
1 TATATATTTATA
*
383511 TATATATTTATG
1 TATATATTTATA
383523 TATATATTT
1 TATATATTT
383532 TTTTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
TATATATTTATA
Found at i:385358 original size:36 final size:37
Alignment explanation
Indices: 385286--385382 Score: 126
Period size: 36 Copynumber: 2.6 Consensus size: 37
385276 GTGCTTGTGG
* * *
385286 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
* *
385323 ATCCTATTTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
385359 ATCCTATTTTT-GAGAGTTTGAATC
1 ATCCTATTTTTAG-GAGTTTGAATC
385383 TAGTAGGACG
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
35 1 0.02
36 30 0.57
37 22 0.42
ACGTcount: A:0.31, C:0.15, G:0.14, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGCAAAATTCT
Found at i:386141 original size:102 final size:99
Alignment explanation
Indices: 385843--386148 Score: 298
Period size: 97 Copynumber: 3.0 Consensus size: 99
385833 AATATTGTTC
* * * * * *
385843 CGAGTCC-ATATCCTCCGCTGTGAAGTTGAAATTGGTTCTAGAACCGGGAAATTGTTGTTGACAG
1 CGAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCT-GAAAC--GAAAATGTTGTTGACAA
* * *
385907 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
63 TCAGCCGTCCCTTC-ATGTGAAGTTGAAC-TGTG-TGTCT
* * * *
385947 CGAGTCTAATATCCTTC-CTGTG-AAGTGAAATTGACTCTG-AACG-AAATCTTGTTGACAATCA
1 CGAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAACGAAAATGTTGTTGACAATCA
* *
386008 GCCGTCACTTCATATGAAGTTGAACTGTGTGTCT
66 GCCGTCCCTTCATGTGAAGTTGAACTGTGTGTCT
*
386042 CGAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAATTGAAAAATGTTTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAA-CG-AAAATG-TTGTTGACAA
* **
386107 CCAGTTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
63 TCAGCCGTCCCTTCA-TGTGAAGTTGAAC-TGTG-TGTCT
386147 CG
1 CG
386149 GTGGCACGAT
Statistics
Matches: 166, Mismatches: 25, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
95 21 0.13
96 9 0.05
97 26 0.16
98 26 0.16
99 2 0.01
101 6 0.04
102 22 0.13
103 24 0.14
104 15 0.09
105 15 0.09
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (99 bp):
CGAGTCCAATATCCTTCGCTGTGAAATTGAAATTGGCTCTGAAACGAAAATGTTGTTGACAATCA
GCCGTCCCTTCATGTGAAGTTGAACTGTGTGTCT
Found at i:386360 original size:213 final size:215
Alignment explanation
Indices: 386068--386459 Score: 542
Period size: 213 Copynumber: 1.8 Consensus size: 215
386058 CGCTGTGAAA
* * ***
386068 TTGAAATTGGCTCTGAAATTGAAAAATGTTTGTTGACAACCAGTTGTCCCTTCATTGTGAAGTTG
1 TTGAAATCGGCTCTGAAATTGAAAAATGTTCGTTGACAACCAACCGTCCCTTCATTGTGAAGTTG
*
386133 AACTTGTGTTGTCTC-GGTGGCACGATATCCTCCATCGTGGAGTTGAAAGCGGAT-GAAACT-GA
66 AACTTGTGTTGTCTCGGGTAGCACGATATCCTCCATCGTGGAGTTGAAAGCGGATCGAAACTGGA
* *
386195 AAAGTTGTTCATTGACAACCAGCCGTCCCTTCG-T-TGAAGTTGGACTTGTGTTTTCTCGGGTAG
131 AAA-TTATT-ATTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTTTCTCGGGTAG
386258 CACGATATCCTCCGTCGTGGAG
194 CACGATATCCTCCGTCGTGGAG
* * ** *
386280 TTGAAATCGGTTCTGGAATTGAGAAGTTGTTCGTTGACAACCAACCGTCCCTTCGTTGTGAAGTT
1 TTGAAATCGGCTCTGAAATTGA-AAAATGTTCGTTGACAACCAACCGTCCCTTCATTGTGAAGTT
* * * *
386345 GAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGTTCCGAAATTG
65 GAACTTGTGTTGTCTCGGGTAGCACGATATCCTCCATCGTGGAGTTGAAAGCGGAT-CGAAACTG
* *
386410 GGAAATTATTATTGGCAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
129 GAAAATTATTATTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
386460 ACTCTAGCTA
Statistics
Matches: 154, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
212 19 0.12
213 51 0.33
214 35 0.23
215 22 0.14
216 10 0.06
217 17 0.11
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (215 bp):
TTGAAATCGGCTCTGAAATTGAAAAATGTTCGTTGACAACCAACCGTCCCTTCATTGTGAAGTTG
AACTTGTGTTGTCTCGGGTAGCACGATATCCTCCATCGTGGAGTTGAAAGCGGATCGAAACTGGA
AAATTATTATTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTTTCTCGGGTAGCA
CGATATCCTCCGTCGTGGAG
Found at i:386372 original size:109 final size:109
Alignment explanation
Indices: 385998--386459 Score: 513
Period size: 109 Copynumber: 4.4 Consensus size: 109
385988 CGAAATCTTG
* * * * * *
385998 TTGACAATCAGCCGTCACTTC-ATATGAAGTTGAAC-TGTG-TGTCTCGAGT--C-CAATATCCT
1 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCT
* * * * * * **
386057 TCG-CTGTGAAATTGAAATTGGCTCTGAAATTGA-AAAATGTTTG
66 CCGTC-GTGGAGTTGAAATCGGTTCTGAAATTGAGAAATTGTTCA
** * *
386100 TTGACAACCAGTTGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTC-GGTGGCACGATATCCT
1 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCT
* * * *
386164 CCATCGTGGAGTTGAAAGCGG--ATGAAACTGA-AAAGTTGTTCA
66 CCGTCGTGGAGTTGAAATCGGTTCTGAAATTGAGAAA-TTGTTCA
* *
386206 TTGACAACCAGCCGTCCCTTCG-T-TGAAGTTGGACTTGTGTTTTCTCGGGTAGCACGATATCCT
1 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCT
* * *
386269 CCGTCGTGGAGTTGAAATCGGTTCTGGAATTGAGAAGTTGTTCG
66 CCGTCGTGGAGTTGAAATCGGTTCTGAAATTGAGAAATTGTTCA
*
386313 TTGACAACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCT
1 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCT
* * *
386378 CCGTCGTGGAGTTGAAATCGGTTCCGAAATTGGGAAATTATT-A
66 CCGTCGTGGAGTTGAAATCGGTTCTGAAATTGAGAAATTGTTCA
*
386421 TTGGCAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
1 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTG
386460 ACTCTAGCTA
Statistics
Matches: 303, Mismatches: 43, Indels: 22
0.82 0.12 0.06
Matches are distributed among these distances:
102 17 0.06
103 12 0.04
104 27 0.09
105 52 0.17
106 24 0.08
107 55 0.18
108 41 0.14
109 75 0.25
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (109 bp):
TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGGGTAGCACGATATCCT
CCGTCGTGGAGTTGAAATCGGTTCTGAAATTGAGAAATTGTTCA
Found at i:386949 original size:66 final size:66
Alignment explanation
Indices: 386877--387020 Score: 204
Period size: 66 Copynumber: 2.2 Consensus size: 66
386867 AAAACGGAAT
* *
386877 TTTGTTTTAAGGGAGATA-AAT-TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCATGGGAGAC
1 TTTGTTTCAAGGGA-A-ACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGT-TCAAGGGAGAC
386940 -AAA
63 AAAA
* *
386943 TTTGTTTCGAGGGAAACAATCTCAAAGGTTTTGTGTTTCAAGAGAAACTGTTCAAGGGAGACAAA
1 TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTTCAAGGGAGACAAA
387008 A
66 A
387009 TTTGTTTCAAGG
1 TTTGTTTCAAGG
387021 AAATTATCTC
Statistics
Matches: 70, Mismatches: 5, Indels: 6
0.86 0.06 0.07
Matches are distributed among these distances:
64 1 0.01
65 14 0.20
66 55 0.79
ACGTcount: A:0.33, C:0.10, G:0.24, T:0.33
Consensus pattern (66 bp):
TTTGTTTCAAGGGAAACAATCTCAAAGATTTTGTGTTTCAAGAGAAACTGTTCAAGGGAGACAAA
A
Found at i:387015 original size:35 final size:33
Alignment explanation
Indices: 386976--387063 Score: 86
Period size: 35 Copynumber: 2.5 Consensus size: 33
386966 AAAGGTTTTG
*
386976 TGTTTCAAGAGAAACTGTTCAAGGGAGACAAAATT
1 TGTTTCAAG-GAAA-TGTTCAAGAGAGACAAAATT
* *
387011 TGTTTCAAGGAAATTATCTCAAGAGAGACGAAATT
1 TGTTTCAAGGAAA-TGT-TCAAGAGAGACAAAATT
**
387046 CATTTCAAGGGAAATGTT
1 TGTTTCAA-GGAAATGTT
387064 TTCATGTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
34 7 0.16
35 32 0.73
36 5 0.11
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (33 bp):
TGTTTCAAGGAAATGTTCAAGAGAGACAAAATT
Found at i:387137 original size:100 final size:101
Alignment explanation
Indices: 386976--387358 Score: 570
Period size: 100 Copynumber: 3.9 Consensus size: 101
386966 AAAGGTTTTG
*
386976 TGTTTCAAGAGAAACTGT-TCAAGGGAGACAAAA-TTTGTTTCAA-GGAAATTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
387038 ACGAAATTCATTTCAAGGGAAATGTTTTC-ATGTTTA
66 AC-AAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
387074 TG-TTCAGGAG-AACTGTCTCAAGGGAGACAAAATTTTGTTTTCAAGGGAAACTATCTCAAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG-TTTCAAGGGAAACTATCTCAAGAGA
*
387137 GACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
65 GAC-AAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
387175 TGTTTCAAGAGAAACTGTCTCAAGGGAGA-AAAATTTTGTTTCAAGGGAAACTATCTTAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
* *
387239 ACAAACTCATTTCAAGGAAAATGTTTTCAATGTTTA
66 ACAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
387275 TGTTTCAAGAGAAACTGTCTCAAGGGA-AAAAAATTTTGTTTCAAGGGAAACTGTCTC-A-AGAG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
**
387337 ACAAAGTTTGTTTCAAGGGAAA
66 ACAAA-TTCATTTCAAGGGAAA
387359 CTGTCTCAAG
Statistics
Matches: 261, Mismatches: 15, Indels: 17
0.89 0.05 0.06
Matches are distributed among these distances:
96 6 0.02
97 22 0.08
98 15 0.06
99 20 0.08
100 129 0.49
101 36 0.14
102 16 0.06
103 17 0.07
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (101 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:387159 original size:36 final size:37
Alignment explanation
Indices: 387084--387159 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 37
387074 TGTTCAGGAG
* * **
387084 AACTGTCTCAAGGGAGACAAAATTTTGTTTTCAAGGGA
1 AACTATCTCAAGAGAGACAAAA-TTTCATTTCAAGGGA
387122 AACTATCTCAAGAGAGACAAAA-TTCATTTCAAGGGA
1 AACTATCTCAAGAGAGACAAAATTTCATTTCAAGGGA
387158 AA
1 AA
387160 TGTTTCCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
36 14 0.41
38 20 0.59
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.25
Consensus pattern (37 bp):
AACTATCTCAAGAGAGACAAAATTTCATTTCAAGGGA
Found at i:387225 original size:36 final size:35
Alignment explanation
Indices: 387084--387373 Score: 159
Period size: 36 Copynumber: 8.5 Consensus size: 35
387074 TGTTCAGGAG
387084 AACTGTCTCAAGGGAGACAAAATTTTGTTTTCAAGGGA
1 AACTGTCTCAA-GGAGA-AAAATTTTG-TTTCAAGGGA
* **
387122 AACTATCTCAAGAGAGACAAAA-TTCATTTCAAGGGA
1 AACTGTCTCAAG-GAGA-AAAATTTTGTTTCAAGGGA
* * *
387158 AA-TGTTTCCAA--TG-----TTTATGTTTCAAGAGA
1 AACTGTCT-CAAGGAGAAAAATTT-TGTTTCAAGGGA
387187 AACTGTCTCAAGGGAGAAAAATTTTGTTTCAAGGGA
1 AACTGTCTCAA-GGAGAAAAATTTTGTTTCAAGGGA
* * * * **
387223 AACTATCTTAAGAGAGACAAA-CTCATTTCAA-GGA
1 AACTGTCTCAAG-GAGAAAAATTTTGTTTCAAGGGA
* * * *
387257 AAATGTTTTCAA--TG-----TTTATGTTTCAAGAGA
1 AACTG-TCTCAAGGAGAAAAATTT-TGTTTCAAGGGA
*
387287 AACTGTCTCAAGGGAAAAAAATTTTGTTTCAAGGGA
1 AACTGTCTCAA-GGAGAAAAATTTTGTTTCAAGGGA
* *
387323 AACTGTCTCAA-GAGACAAAGTTTGTTTCAAGGGA
1 AACTGTCTCAAGGAGAAAAATTTTGTTTCAAGGGA
387357 AACTGTCTCAAGAGAGA
1 AACTGTCTCAAG-GAGA
387374 CAATGGTGAG
Statistics
Matches: 189, Mismatches: 35, Indels: 58
0.67 0.12 0.21
Matches are distributed among these distances:
28 3 0.02
29 25 0.13
30 10 0.05
32 2 0.01
33 1 0.01
34 37 0.20
35 15 0.08
36 68 0.36
37 9 0.05
38 19 0.10
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (35 bp):
AACTGTCTCAAGGAGAAAAATTTTGTTTCAAGGGA
Found at i:387352 original size:34 final size:34
Alignment explanation
Indices: 387275--387371 Score: 140
Period size: 34 Copynumber: 2.8 Consensus size: 34
387265 TCAATGTTTA
* * *
387275 TGTTTCAAGAGAAACTGTCTCAAGGGAAAAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAA--GAGAAAAAGTT
*
387311 TGTTTCAAGGGAAACTGTCTCAAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAAAAAGTT
387345 TGTTTCAAGGGAAACTGTCTCAAGAGA
1 TGTTTCAAGGGAAACTGTCTCAAGAGA
387372 GACAATGGTG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
34 35 0.61
36 22 0.39
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (34 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAAAAAGTT
Found at i:388251 original size:22 final size:22
Alignment explanation
Indices: 388226--388276 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
388216 TTGTGTTTGG
388226 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
388248 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
388270 TCAAAGG
1 TCAAAGG
388277 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:388896 original size:20 final size:19
Alignment explanation
Indices: 388871--388933 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 19
388861 CTTTTGTTCC
*
388871 CTTTTTTATTTTTGTTCTTT
1 CTTTTTT-TTCTTGTTCTTT
*
388891 CTTTTTTTTCTTGTTTTTT
1 CTTTTTTTTCTTGTTCTTT
* * *
388910 C-CTTTTTGCTTCTT-TTT
1 CTTTTTTTTCTTGTTCTTT
388927 CTTTTTT
1 CTTTTTT
388934 CTTTTGCCCT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 4 0.11
18 14 0.39
19 11 0.31
20 7 0.19
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (19 bp):
CTTTTTTTTCTTGTTCTTT
Found at i:388923 original size:30 final size:30
Alignment explanation
Indices: 388889--388952 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
388879 TTTTTGTTCT
* **
388889 TTCTTTTT-TTTCTTGTTTTTTCCTTTTTG
1 TTCTTTTTCTTTCTTCTTTTGCCCTTTTTG
*
388918 CTTCTTTTTCTTTTTTCTTTTGCCCTTTTTG
1 -TTCTTTTTCTTTCTTCTTTTGCCCTTTTTG
388949 TTCT
1 TTCT
388953 GATTGAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 12 0.41
31 17 0.59
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.75
Consensus pattern (30 bp):
TTCTTTTTCTTTCTTCTTTTGCCCTTTTTG
Found at i:389910 original size:21 final size:21
Alignment explanation
Indices: 389884--389949 Score: 105
Period size: 21 Copynumber: 3.1 Consensus size: 21
389874 GATTTCTGGG
389884 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
389905 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
* * *
389926 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAATCGGTACCCATT
389947 CAA
1 CAA
389950 ACGAACAACA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.30, C:0.27, G:0.26, T:0.17
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:390670 original size:31 final size:31
Alignment explanation
Indices: 390623--390745 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
390613 AGGGTCGAGG
390623 GTTTACCTA--TTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
390652 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
390683 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
390714 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
390745 G
1 G
390746 GTCCTTCGGG
Statistics
Matches: 86, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
29 9 0.10
31 76 0.88
32 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:393875 original size:21 final size:21
Alignment explanation
Indices: 393849--393893 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
393839 GATTTCTGGG
* *
393849 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
393870 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
393891 CAA
1 CAA
393894 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:394680 original size:62 final size:62
Alignment explanation
Indices: 394560--394684 Score: 182
Period size: 62 Copynumber: 2.0 Consensus size: 62
394550 AAGGTCGAGG
* * * *
394560 GTTTACCTATGTTCTTCGGGACATATGGACTGTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
394622 GTTTACCTATG-TCATTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAATC-TATGGACT
1 GTTTACCTATGTTC-TTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAA-CATATGGACT
394684 G
1 G
394685 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
61 2 0.04
62 54 0.95
63 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (62 bp):
GTTTACCTATGTTCTTCGGGACATATGGACTGATTACCTAGGTTCTTCAGAACATATGGACT
Found at i:394684 original size:31 final size:31
Alignment explanation
Indices: 394560--394669 Score: 186
Period size: 31 Copynumber: 3.5 Consensus size: 31
394550 AAGGTCGAGG
394560 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
394591 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
394622 GTTTACCTATG-TCATTCGGGACATATGGACT
1 GTTTACCTATGTTC-TTCGGGACATATGGACT
* *
394653 GATTACCTAGGTTCTTC
1 GTTTACCTATGTTCTTC
394670 AGAATCTATG
Statistics
Matches: 75, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
30 2 0.03
31 71 0.95
32 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:398778 original size:21 final size:23
Alignment explanation
Indices: 398754--398802 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
398744 ATTTATACGT
398754 TAATAGTAAT-AATA-ATAAATA
1 TAATAGTAATAAATATATAAATA
* *
398775 TAATAGTTATAAATATATATATA
1 TAATAGTAATAAATATATAAATA
398798 TAATA
1 TAATA
398803 ACTTTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.38
22 4 0.17
23 11 0.46
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (23 bp):
TAATAGTAATAAATATATAAATA
Found at i:399351 original size:36 final size:37
Alignment explanation
Indices: 399270--399367 Score: 110
Period size: 37 Copynumber: 2.6 Consensus size: 37
399260 GTGCTTGTGG
* * **
399270 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTATTTTTAGGAGTTGAATCCATAGCAAAATTCT
* *
399307 ATCATATTTTTAGGAGTTGAATCCA-AGCATAATTCT
1 ATCCTATTTTTAGGAGTTGAATCCATAGCAAAATTCT
399343 ATCCTATTTTT-GAGAGTTTGAATCC
1 ATCCTATTTTTAG-GAG-TTGAATCC
399368 TAGTAGGATG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 1 0.02
36 23 0.44
37 28 0.54
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTGAATCCATAGCAAAATTCT
Found at i:408403 original size:3 final size:3
Alignment explanation
Indices: 408395--408430 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
408385 CCTTTTATCT
408395 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
408431 TCTTATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TTA
Found at i:408509 original size:21 final size:20
Alignment explanation
Indices: 408485--408536 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
408475 TTTTTTAATC
*
408485 ATTTTATTATTTTATTTCTTT
1 ATTTTATTA-GTTATTTCTTT
408506 ATTTTTATTAGTTATTTCTTT
1 A-TTTTATTAGTTATTTCTTT
408527 ATTTCTATTA
1 ATTT-TATTA
408537 CTTTGTTATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 3 0.11
21 17 0.61
22 8 0.29
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (20 bp):
ATTTTATTAGTTATTTCTTT
Found at i:408556 original size:2 final size:2
Alignment explanation
Indices: 408549--408598 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
408539 TTGTTATACG
*
408549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
408591 TA TA TA TA
1 TA TA TA TA
408599 GTTATCTTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:408822 original size:5 final size:5
Alignment explanation
Indices: 408812--408868 Score: 64
Period size: 5 Copynumber: 11.8 Consensus size: 5
408802 ATTTAACTTC
* * *
408812 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -CTTT ATCTT ATCTT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
*
408860 ATTTC ATTT
1 ATTTT ATTT
408869 GTTTTTAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
4 6 0.13
5 39 0.87
ACGTcount: A:0.18, C:0.07, G:0.00, T:0.75
Consensus pattern (5 bp):
ATTTT
Found at i:408830 original size:15 final size:14
Alignment explanation
Indices: 408813--408891 Score: 79
Period size: 14 Copynumber: 5.6 Consensus size: 14
408803 TTTAACTTCA
408813 TTTTATTTTATTTT
1 TTTTATTTTATTTT
408827 ATTTTATTTTATTTT
1 -TTTTATTTTATTTT
* * *
408842 CTTTATCTTATCTT
1 TTTTATTTTATTTT
*
408856 TTTTATTTCATTTGT
1 TTTTATTTTATTT-T
* *
408871 TTTTA-ATTGTTTT
1 TTTTATTTTATTTT
408884 TTTTATTT
1 TTTTATTT
408892 ACTTTCATTA
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
13 6 0.12
14 25 0.49
15 20 0.39
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTATTTTATTTT
Found at i:410326 original size:203 final size:204
Alignment explanation
Indices: 409977--410384 Score: 809
Period size: 203 Copynumber: 2.0 Consensus size: 204
409967 CTACCCTCCT
409977 AGAACTAGTGGCTTTTTCATTGCCGAGCTTAGATAACGAGCAGCTCTTGCCCCAAGGCTGCGAGG
1 AGAACTAGTGGCTTTTTCATTGCCGAGCTTAGATAACGAGCAGCTCTTGCCCCAAGGCTGCGAGG
410042 CCACCGTGGATATACCTTCCGAGAATATCCAATACCTGAAGATTGCCTACGATTTGCTTCGACAT
66 CCACCGTGGATATACCTTCCGAGAATATCCAATACCTGAAGATTGCCTACGATTTGCTTCGACAT
410107 CCGGTGAAGCAGTTCGTCATAGATCAAAAGCCGGATTGGATATTGGCTGATGTGAT-CCTTACTG
131 CCGGTGAAGCAGTTCGTCATAGATCAAAAGCCGGATTGGATATTGGCTGATGTGATCCCTTACTG
410171 GGTGGTGGA
196 GGTGGTGGA
410180 AGAACTAGTGGCTTTTTCATTGCCGAGCTTAGATAACGAGCAGCTCTTGCCCCAAGGCTGCGAGG
1 AGAACTAGTGGCTTTTTCATTGCCGAGCTTAGATAACGAGCAGCTCTTGCCCCAAGGCTGCGAGG
410245 CCACCGTGGATATACCTTCCGAGAATATCCAATACCTGAAGATTGCCTACGATTTGCTTCGACAT
66 CCACCGTGGATATACCTTCCGAGAATATCCAATACCTGAAGATTGCCTACGATTTGCTTCGACAT
410310 CCGGTGAAGCAGTTCGTCATAGATCAAAAGCCGGATTGGATATTGGCTGATGTGATCCCTTACTG
131 CCGGTGAAGCAGTTCGTCATAGATCAAAAGCCGGATTGGATATTGGCTGATGTGATCCCTTACTG
410375 GGTGGTGGA
196 GGTGGTGGA
410384 A
1 A
410385 AGCTAAGGAA
Statistics
Matches: 204, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
203 186 0.91
204 18 0.09
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (204 bp):
AGAACTAGTGGCTTTTTCATTGCCGAGCTTAGATAACGAGCAGCTCTTGCCCCAAGGCTGCGAGG
CCACCGTGGATATACCTTCCGAGAATATCCAATACCTGAAGATTGCCTACGATTTGCTTCGACAT
CCGGTGAAGCAGTTCGTCATAGATCAAAAGCCGGATTGGATATTGGCTGATGTGATCCCTTACTG
GGTGGTGGA
Found at i:415531 original size:176 final size:175
Alignment explanation
Indices: 415236--415576 Score: 612
Period size: 177 Copynumber: 1.9 Consensus size: 175
415226 TAAAAATAAA
415236 TGATCTCTAACGTTATCGATCGTTCGACTTAAATTCCATTAAATTCTTCGAAATCATCATAGTTC
1 TGATCTCTAACGTTATCGATCGTTCGACTTAAATTCCATTAAATTCTTCGAAATCATCATAGTTC
*
415301 CTCCATTTATCATGAGAGGCAATTTCGATTTATCTTTTCATCACCTTGATGTTATATATATTCAC
66 CTCCATTTATCATGAGAGGCAATTTCGATTTATCTTTTCATCACCTCGATG-T-TATATATTCAC
* *
415366 AACGCTGTTTAGAAATGCATTTTCGTCTGATAATGATCTGCGTTTGG
129 AAAGCTATTTAGAAATGCATTTTCGTCTGATAATGATCTGCGTTTGG
*
415413 TGATCTCTAACGTTATCGATCGTTCGATTTAAATTCCATTAAATTCTTCGAAATCATC-TAGTTC
1 TGATCTCTAACGTTATCGATCGTTCGACTTAAATTCCATTAAATTCTTCGAAATCATCATAGTTC
415477 CTCCATTTATCATGAGAGGCAATTTCGATTTATCTTTTCATCACCTCGATGTTATATATTCACAA
66 CTCCATTTATCATGAGAGGCAATTTCGATTTATCTTTTCATCACCTCGATGTTATATATTCACAA
*
415542 AGCTATTTAGAAATGCATTTTCGTTTGATAATGAT
131 AGCTATTTAGAAATGCATTTTCGTCTGATAATGAT
415577 GGAATCCATG
Statistics
Matches: 159, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
174 45 0.28
175 1 0.01
176 56 0.35
177 57 0.36
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (175 bp):
TGATCTCTAACGTTATCGATCGTTCGACTTAAATTCCATTAAATTCTTCGAAATCATCATAGTTC
CTCCATTTATCATGAGAGGCAATTTCGATTTATCTTTTCATCACCTCGATGTTATATATTCACAA
AGCTATTTAGAAATGCATTTTCGTCTGATAATGATCTGCGTTTGG
Found at i:415955 original size:41 final size:42
Alignment explanation
Indices: 415890--415985 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 42
415880 TTTCTTGTAA
* * * *
415890 AAACGCCGCAATATATTTGAAATTTTGCGGCGTTTTAG-CC-T
1 AAACGCCGCAATAGAGTTGAAATTTAGCGGC-ATTTAGACCAT
*
415931 AAACGCCGCAATAGAGTTGTAATTTAGCGGCATTTAGACCAT
1 AAACGCCGCAATAGAGTTGAAATTTAGCGGCATTTAGACCAT
415973 AAACGCCGCAATA
1 AAACGCCGCAATA
415986 AGTATTTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 5 0.10
41 29 0.60
42 14 0.29
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (42 bp):
AAACGCCGCAATAGAGTTGAAATTTAGCGGCATTTAGACCAT
Found at i:416448 original size:21 final size:21
Alignment explanation
Indices: 416424--416474 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
416414 AGTGTTTTAC
416424 TGGTTTACTGCTTGGGAGCAA
1 TGGTTTACTGCTTGGGAGCAA
416445 TGGTTTACTGCTTGGGAGCAA
1 TGGTTTACTGCTTGGGAGCAA
*
416466 TGTTTTACT
1 TGGTTTACT
416475 ACTTTCGAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.29, T:0.39
Consensus pattern (21 bp):
TGGTTTACTGCTTGGGAGCAA
Found at i:418212 original size:20 final size:20
Alignment explanation
Indices: 418167--418224 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
418157 GCATGGGTAG
418167 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
418191 TGTATCGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
418211 TGCATCGATGCACT
1 TGCATCGATGCACT
418225 TCAAGGGGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 2 0.06
24 12 0.38
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:419262 original size:29 final size:30
Alignment explanation
Indices: 419136--419259 Score: 151
Period size: 30 Copynumber: 4.1 Consensus size: 30
419126 TCGAGACATA
* * * * *
419136 TGGACAGTTTACCTAGGTTCTTCAGGACCTA
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
419167 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
419197 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * *
419227 TGGATAGTTACCG-GGGTCTATGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
419256 TGGA
1 TGGA
419260 TAGGTCCTTC
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
29 17 0.20
30 60 0.71
31 7 0.08
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:419537 original size:2 final size:2
Alignment explanation
Indices: 419530--419578 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
419520 GTATGCGTGG
419530 AT AT AT AT -T 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
419571 AT AT AT AT
1 AT AT AT AT
419579 GAAAGGTGCA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:425687 original size:21 final size:21
Alignment explanation
Indices: 425643--425688 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
425633 CGGAAGTAAT
*
425643 GAGAGAAGCAGCGATAGCATA
1 GAGAGAAGCAGCCATAGCATA
*
425664 GAGAGAAGCA-CCATATCATCA
1 GAGAGAAGCAGCCATAGCAT-A
425685 GAGA
1 GAGA
425689 TATGAAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.43, C:0.17, G:0.28, T:0.11
Consensus pattern (21 bp):
GAGAGAAGCAGCCATAGCATA
Found at i:426139 original size:44 final size:44
Alignment explanation
Indices: 426023--426150 Score: 148
Period size: 44 Copynumber: 2.9 Consensus size: 44
426013 AAATGTTGCA
* * *** * *
426023 ATATACCATACATTTAGCGATGTTTGTAGGATACAAACGTCACT
1 ATATACCAGACCTTTAGCGATGTTTGTATCCTAAAAACGCCACT
* **
426067 ATATATCAGACCTTTAGCGGCGTTTGTATCCTAAAAACGCCACT
1 ATATACCAGACCTTTAGCGATGTTTGTATCCTAAAAACGCCACT
* *
426111 ATATACCAGACCTTTAGCGATATTTGTATTCTAAAAACGC
1 ATATACCAGACCTTTAGCGATGTTTGTATCCTAAAAACGC
426151 TGTTTAGCGA
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 69 1.00
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (44 bp):
ATATACCAGACCTTTAGCGATGTTTGTATCCTAAAAACGCCACT
Found at i:426159 original size:30 final size:30
Alignment explanation
Indices: 426123--426182 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
426113 ATACCAGACC
* *
426123 TTTAGCGATATTTGTATTC-TAAAAACGCTG
1 TTTAGCGACATTTGTA-TCAAAAAAACGCTG
*
426153 TTTAGCGACGTTTGTATCAAAAAAACGCTG
1 TTTAGCGACATTTGTATCAAAAAAACGCTG
426183 CCAAATTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 2 0.08
30 24 0.92
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (30 bp):
TTTAGCGACATTTGTATCAAAAAAACGCTG
Found at i:426261 original size:43 final size:42
Alignment explanation
Indices: 426185--426424 Score: 250
Period size: 43 Copynumber: 5.6 Consensus size: 42
426175 AAACGCTGCC
* **
426185 AAATTTCAACACCTATTGCGGCGTTTGCAAGAAAAATCCTGCT
1 AAATCTCAACACCTATTGCGGCGTTTGTGAGAAAAATCC-GCT
* * * * *
426228 ACATCTCAAAACTTATTGCGGCGTTTTTGAGAAAAGTGCCGCT
1 AAATCTCAACACCTATTGCGGCGTTTGTGAGAAAAAT-CCGCT
* * * * * *
426271 AAATCTCTACACTTATTGTGGCGTTTTTGAGAAAAACGCCGCG
1 AAATCTCAACACCTATTGCGGCGTTTGTGAGAAAAA-TCCGCT
** *
426314 AAATAGCAACACCTATTGCGGCGTTTGTGATAAAAATGCCGCT
1 AAATCTCAACACCTATTGCGGCGTTTGTGAGAAAAAT-CCGCT
*
426357 AAATCTCAACACCTATTGCGGCGTTTGT-AGAAAAAAACCGCT
1 AAATCTCAACACCTATTGCGGCGTTTGTGAG-AAAAATCCGCT
426399 AAA-CATCAACACCTATTGCGGCGTTT
1 AAATC-TCAACACCTATTGCGGCGTTT
426425 TTCGTTAACA
Statistics
Matches: 164, Mismatches: 28, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.01
42 30 0.18
43 131 0.80
44 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (42 bp):
AAATCTCAACACCTATTGCGGCGTTTGTGAGAAAAATCCGCT
Found at i:437295 original size:21 final size:21
Alignment explanation
Indices: 437271--437342 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
437261 TCGAAGTTCG
437271 CGTTGCGATTTATTCCAAATT
1 CGTTGCGATTTATTCCAAATT
* *
437292 CGTTGC-A-ATAGTCCAAATT
1 CGTTGCGATTTATTCCAAATT
*
437311 CGCGTTGCGATTTATTCCAAGTT
1 --CGTTGCGATTTATTCCAAATT
*
437334 TGTTGCGAT
1 CGTTGCGAT
437343 AGAAAACAAG
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
19 10 0.24
20 1 0.02
21 20 0.49
22 1 0.02
23 9 0.22
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.39
Consensus pattern (21 bp):
CGTTGCGATTTATTCCAAATT
Found at i:437303 original size:42 final size:42
Alignment explanation
Indices: 437257--437344 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
437247 GTTCATTGTG
* *
437257 ATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCA
1 ATAGTCCAAATTCGCGTTGCGATTTATTCCAAATTCGTTGCA
* * *
437299 ATAGTCCAAATTCGCGTTGCGATTTATTCCAAGTTTGTTGCG
1 ATAGTCCAAATTCGCGTTGCGATTTATTCCAAATTCGTTGCA
437341 ATAG
1 ATAG
437345 AAAACAAGGG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (42 bp):
ATAGTCCAAATTCGCGTTGCGATTTATTCCAAATTCGTTGCA
Found at i:437518 original size:23 final size:21
Alignment explanation
Indices: 437487--437555 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
437477 ACTATTACAA
*
437487 CGAATTTGGAATAAATCGCAACG
1 CGAACTTGGAAT--ATCGCAACG
*
437510 CGAACTTGGACTATCGCAACG
1 CGAACTTGGAATATCGCAACG
* *
437531 CGAACTTGGACTATCGCAATG
1 CGAACTTGGAATATCGCAACG
437552 CGAA
1 CGAA
437556 TATGTAAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
21 33 0.77
23 10 0.23
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (21 bp):
CGAACTTGGAATATCGCAACG
Found at i:437525 original size:21 final size:21
Alignment explanation
Indices: 437501--437555 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
437491 TTTGGAATAA
437501 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
437522 ATCGCAACGCGAACTTGGACT
1 ATCGCAACGCGAACTTGGACT
*
437543 ATCGCAATGCGAA
1 ATCGCAACGCGAA
437556 TATGTAAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.24, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTGGACT
Found at i:437568 original size:20 final size:20
Alignment explanation
Indices: 437543--437614 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
437533 AACTTGGACT
437543 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
437563 ATCGCAATGAGAATATGTAT
1 ATCGCAATGCGAATATGTAA
437583 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
437603 ATCGCAATGCGA
1 ATCGCAATGCGA
437615 TAGTCGAAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:439719 original size:34 final size:32
Alignment explanation
Indices: 439698--439775 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 32
439688 AGTATTTTTT
439698 TAAATAGTTATTATTTTTTATATAATATATTATG
1 TAAATA-TTATT-TTTTTTATATAATATATTATG
* *
439732 TAAATATTATTTTTTTTAAAATAATAT-TTATA
1 TAAATATTATTTTTTTT-ATATAATATATTATG
*
439764 TAATTATTATTT
1 TAAATATTATTT
439776 ATTTAGAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
32 21 0.52
33 13 0.32
34 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.58
Consensus pattern (32 bp):
TAAATATTATTTTTTTTATATAATATATTATG
Found at i:439728 original size:19 final size:18
Alignment explanation
Indices: 439693--439756 Score: 55
Period size: 16 Copynumber: 3.7 Consensus size: 18
439683 ATATTAGTAT
*
439693 TTTTTTAAATAGTTATTA
1 TTTTTTAAATAATTATTA
*
439711 TTTTTTATATAA-TA-TA
1 TTTTTTAAATAATTATTA
* *
439727 TTATGTAAAT-ATTATT-
1 TTTTTTAAATAATTATTA
439743 TTTTTTAAAATAAT
1 TTTTTT-AAATAAT
439757 ATTTATATAA
Statistics
Matches: 35, Mismatches: 7, Indels: 8
0.70 0.14 0.16
Matches are distributed among these distances:
15 1 0.03
16 15 0.43
17 7 0.20
18 12 0.34
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (18 bp):
TTTTTTAAATAATTATTA
Found at i:439730 original size:22 final size:20
Alignment explanation
Indices: 439682--439730 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
439672 AAATTTATTT
*
439682 TATATTAGTATTTTTTTAAA
1 TATATTATTATTTTTTTAAA
*
439702 TA-GTTATTATTTTTTATATAA
1 TATATTATTATTTTTT-TA-AA
439723 TATATTAT
1 TATATTAT
439731 GTAAATATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.48
20 4 0.17
21 4 0.17
22 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (20 bp):
TATATTATTATTTTTTTAAA
Found at i:439742 original size:30 final size:32
Alignment explanation
Indices: 439706--439780 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 32
439696 TTTAAATAGT
* *
439706 TATTATTTTTTATATAAT-ATA-TTATGTAAA
1 TATTATTTTTTATAAAATAATATTTATATAAA
* *
439736 TATTATTTTTTTTAAAATAATATTTATATAAT
1 TATTATTTTTTATAAAATAATATTTATATAAA
439768 TATTATTTATTTA
1 TATTATTT-TTTA
439781 GAATTATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 16 0.43
31 3 0.08
32 15 0.41
33 3 0.08
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (32 bp):
TATTATTTTTTATAAAATAATATTTATATAAA
Found at i:441490 original size:21 final size:21
Alignment explanation
Indices: 441460--441507 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
441450 GCAGGGGTAC
* *
441460 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
441481 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
441502 ATGCCA
1 ATGCCA
441508 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:441537 original size:21 final size:21
Alignment explanation
Indices: 441511--441583 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
441501 TATGCCATCT
*
441511 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
441532 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
441553 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
441574 CCGCAGGGTT
1 CCGCAGGGTT
441584 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:442157 original size:34 final size:34
Alignment explanation
Indices: 442107--442203 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
442097 AATGTTTTTT
*
442107 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
442141 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
442174 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
442204 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:442210 original size:34 final size:33
Alignment explanation
Indices: 442105--442210 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
442095 TAAATGTTTT
*
442105 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
442139 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
442171 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
442206 TTAAA
1 TTAAA
442211 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:442873 original size:127 final size:127
Alignment explanation
Indices: 442595--443600 Score: 1910
Period size: 127 Copynumber: 7.9 Consensus size: 127
442585 AGTTATTCAA
442595 ACTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
442659 GACGAAATAATGGAAGGCGC-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
442720 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
442785 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
* *
442847 ACTGATATGTCTAGTGTCCCCGAGGGACATAAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
442912 GACGAAATAATGGAAGGCGCGCCCC-GGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
442973 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
443038 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
443100 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
443165 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
* *
443227 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATATTATCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
443292 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
66 GACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
443355 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
* *
443420 GACGAAATAATGGAAGGCGCGTCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGAT
66 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
*
443482 ACTGATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
443547 GACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GACGAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAA
443601 CCGATTATAG
Statistics
Matches: 864, Mismatches: 12, Indels: 7
0.98 0.01 0.01
Matches are distributed among these distances:
125 17 0.02
126 191 0.22
127 500 0.58
128 156 0.18
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (127 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:443060 original size:253 final size:255
Alignment explanation
Indices: 442595--443600 Score: 1914
Period size: 253 Copynumber: 4.0 Consensus size: 255
442585 AGTTATTCAA
442595 ACTGATATATCTAGTGT-CCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
442659 GACGAAATAATGGAAGGCGC-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
66 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
442723 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
131 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
442788 GAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
196 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
* *
442847 ACTGATATGTCTAGTGTCCCCGAGGGACATAAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
442912 GACGAAATAATGGAAGGCGCGCCCC-GGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
66 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
442976 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
131 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
443041 GAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
196 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
443100 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
443165 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
66 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
* *
443230 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATATTATCTGAC
131 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
443295 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
196 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
443355 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
1 ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
* *
443420 GACGAAATAATGGAAGGCGCGTCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGATACT
66 GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
*
443485 GATATATCTAGTGTCCCCGAGGGACATGAATGACATAATAGGGCAATGATAACATATTCTCTGAC
131 GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
443550 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
196 GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
443601 CCGATTATAG
Statistics
Matches: 739, Mismatches: 11, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
252 16 0.02
253 317 0.43
254 124 0.17
255 282 0.38
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (255 bp):
ACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT
GACGAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACT
GATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGAC
GAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGT
Found at i:443681 original size:8 final size:8
Alignment explanation
Indices: 443668--443708 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
443658 TCACAATCTT
443668 TCAAATTC
1 TCAAATTC
443676 TCAAATTC
1 TCAAATTC
* *
443684 CCAAACTC
1 TCAAATTC
443692 T-AAATTC
1 TCAAATTC
443699 TCAAATTC
1 TCAAATTC
443707 TC
1 TC
443709 TGAAATGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:455126 original size:19 final size:19
Alignment explanation
Indices: 455102--455175 Score: 94
Period size: 19 Copynumber: 3.9 Consensus size: 19
455092 AATGACCAAC
* *
455102 TAAATCGTAATGCGATCGA
1 TAAATCGCAACGCGATCGA
* *
455121 TAAATCGTAATGCGATCGA
1 TAAATCGCAACGCGATCGA
*
455140 TAATTCGCAACGCGATCGA
1 TAAATCGCAACGCGATCGA
*
455159 TAATTCGCAACGCGATC
1 TAAATCGCAACGCGATC
455176 TCCGGTATCG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (19 bp):
TAAATCGCAACGCGATCGA
Found at i:455286 original size:32 final size:32
Alignment explanation
Indices: 455222--455286 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
455212 GATTCTGACT
* **
455222 ATCGCATTGCAATTTCCCAAATTCGCGTTGCG
1 ATCGCAATGCAATTTCCCAAATTCGCAATGCG
* * *
455254 ATCGCAATGCGATTTTCCTAATTCGCAATGCG
1 ATCGCAATGCAATTTCCCAAATTCGCAATGCG
455286 A
1 A
455287 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (32 bp):
ATCGCAATGCAATTTCCCAAATTCGCAATGCG
Found at i:455301 original size:20 final size:20
Alignment explanation
Indices: 455276--455382 Score: 128
Period size: 20 Copynumber: 5.3 Consensus size: 20
455266 TTTTCCTAAT
455276 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
455296 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
455317 TCAG-AATGCGATTACGTAAA
1 TC-GCAATGCGAATACGTAAA
455337 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
455357 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
455377 TCGCAA
1 TCGCAA
455383 CGAGATTCTG
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
19 2 0.03
20 57 0.78
21 13 0.18
22 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:455325 original size:41 final size:40
Alignment explanation
Indices: 455276--455384 Score: 132
Period size: 41 Copynumber: 2.7 Consensus size: 40
455266 TTTTCCTAAT
**
455276 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAA-TACGAAAA
* * *
455317 TCAG-AATGCGATTACGTAAATCGCAATGCGAATACGTAAA
1 TC-GCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
455357 TCGCAATGCGAAT-CTGTAAATCGCAACG
1 TCGCAATGCGAATAC-GTAAATCGCAACG
455385 AGATTCTGAC
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
39 2 0.03
40 27 0.47
41 28 0.48
42 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATACGAAAA
Found at i:455392 original size:20 final size:20
Alignment explanation
Indices: 455332--455392 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
455322 ATGCGATTAC
* *
455332 GTAAATCGCAATGCGAATAC-
1 GTAAATCGCAACGAGAAT-CT
* *
455352 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGAGAATCT
*
455372 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGAGAATCT
455392 G
1 G
455393 ACTATCGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 1 0.03
20 36 0.97
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (20 bp):
GTAAATCGCAACGAGAATCT
Found at i:456272 original size:24 final size:24
Alignment explanation
Indices: 456245--456298 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
456235 GTATTCAAAA
456245 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
456269 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
456293 TTTGAT
1 TTTGAT
456299 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:458756 original size:20 final size:20
Alignment explanation
Indices: 458731--458819 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
458721 CAACGCGGAA
458731 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
458751 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* * * *
458771 ATCGTAATGTGGAATTGACT
1 ATCGCAACGCGGAAATGACT
*
458791 ATCGCAATGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
458811 ATCGCAACG
1 ATCGCAACG
458820 AGATAATCGC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 55 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:458848 original size:33 final size:34
Alignment explanation
Indices: 458791--458886 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
458781 GGAATTGACT
* **
458791 ATCGCAATGCGGAAATGACTATCGCAACGAGAT-A
1 ATCGCAATGCGAAAATGAAAATCGCAACGAG-TGA
*
458825 ATCGCAATGC-TAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAAATGAAAATCGCAACGAGTGA
458858 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCGAAAATGAAAATCGCAACG
458887 CGAAATTAGT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
32 1 0.02
33 28 0.50
34 27 0.48
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.17
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGAAAATCGCAACGAGTGA
Found at i:458970 original size:33 final size:33
Alignment explanation
Indices: 458901--458996 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
458891 ATTAGTTTCG
* *
458901 CGTTGCGATTTTCATTTTCGCATTTCAATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
458935 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
* ** *
458968 CGTTGTGATAGTCATTTCAGCGTTGCGAT
1 CGTTGCGATTTTCATTTC-GCATTGCGAT
458997 AGTCTGTTTT
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 31 0.57
34 23 0.43
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:459117 original size:14 final size:14
Alignment explanation
Indices: 459098--459134 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
459088 CATCAATTAA
459098 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
459112 ACAAATCATCTTTT
1 ACAAATCAACATTT
459126 ACAAATCAA
1 ACAAATCAA
459135 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:460551 original size:42 final size:42
Alignment explanation
Indices: 460486--460568 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
460476 TCTAGAATGT
*
460486 TGGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGG
** *
460528 TGGGAGGGGA-CTCTTCAGGGATGATAGGGGCCTCTTGAACG
1 TGGGA-GGGACCTCTTCAACGATGACAGGGGCCTCTTGAACG
460569 ATAGGGGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
42 32 0.89
43 4 0.11
ACGTcount: A:0.20, C:0.20, G:0.37, T:0.22
Consensus pattern (42 bp):
TGGGAGGGACCTCTTCAACGATGACAGGGGCCTCTTGAACGG
Found at i:460584 original size:42 final size:42
Alignment explanation
Indices: 460486--460597 Score: 111
Period size: 42 Copynumber: 2.7 Consensus size: 42
460476 TCTAGAATGT
* *
460486 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTCAACGATGACAGGGGCCTCTTGAACGA
* * ** *
460528 TGGGAGGGGACTCTTCAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTCAACGATGACAGGGGCCTCTTGAACGA
* *
460570 TAGGG-GAGGCCTCTTGAATGATGACAGG
1 T-GGGAGAGGCCTCTTCAACGATGACAGG
460598 TGAGTCGGGC
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
42 51 0.91
43 5 0.09
ACGTcount: A:0.22, C:0.19, G:0.38, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTCAACGATGACAGGGGCCTCTTGAACGA
Found at i:461134 original size:33 final size:34
Alignment explanation
Indices: 461074--461170 Score: 142
Period size: 33 Copynumber: 2.9 Consensus size: 34
461064 TCTGAAACTT
* *
461074 AAAATCGCAACGCGAAAATGACTATCGCAACGAG
1 AAAATCGCAACGCGAAAATGACTATCGCAACAAC
* **
461108 AGAATCGCAACGC-AAAATGAAAATCGCAACAAC
1 AAAATCGCAACGCGAAAATGACTATCGCAACAAC
461141 AAAATCGCAACGCGAAAATGACTATCGCAA
1 AAAATCGCAACGCGAAAATGACTATCGCAA
461171 TGCGAATTTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
33 28 0.52
34 26 0.48
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (34 bp):
AAAATCGCAACGCGAAAATGACTATCGCAACAAC
Found at i:461169 original size:20 final size:20
Alignment explanation
Indices: 461144--461192 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
461134 CAACAACAAA
461144 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
461164 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
461184 ATCGCAACG
1 ATCGCAACG
461193 AGAGAATCGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:461260 original size:34 final size:34
Alignment explanation
Indices: 461216--461329 Score: 120
Period size: 34 Copynumber: 3.2 Consensus size: 34
461206 GCAATTTTCA
*
461216 TTTCGCATTACGATTCTTTCGTTGCAATAGTCAT
1 TTTCGCATTACGATTCTTTCGTTGCGATAGTCAT
*
461250 TTTCGTATTACGATAGTCATTTTCGCATTGCGATAGTCAT
1 TTTCGCATTACGAT--TC--TTTCG--TTGCGATAGTCAT
** * *
461290 TTTCGCATTGTGATTCTCTCATTGCGATAGTCAT
1 TTTCGCATTACGATTCTTTCGTTGCGATAGTCAT
461324 TTTCGC
1 TTTCGC
461330 GTTGAGATAG
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
34 32 0.48
36 5 0.07
38 7 0.10
40 23 0.34
ACGTcount: A:0.19, C:0.20, G:0.17, T:0.44
Consensus pattern (34 bp):
TTTCGCATTACGATTCTTTCGTTGCGATAGTCAT
Found at i:461267 original size:20 final size:20
Alignment explanation
Indices: 461242--461360 Score: 117
Period size: 20 Copynumber: 6.2 Consensus size: 20
461232 TTTCGTTGCA
*
461242 ATAGTCATTTTCGTATTACG
1 ATAGTCATTTTCGCATTACG
*
461262 ATAGTCATTTTCGCATTGCG
1 ATAGTCATTTTCGCATTACG
461282 ATAGTCATTTTCGCATT--G
1 ATAGTCATTTTCGCATTACG
* * *
461300 -T-G--ATTCTCTCATTGCG
1 ATAGTCATTTTCGCATTACG
*
461316 ATAGTCATTTTCGCGTTGA-G
1 ATAGTCATTTTCGCATT-ACG
*
461336 ATAGTCATTTTCGCATTGCG
1 ATAGTCATTTTCGCATTACG
461356 ATAGT
1 ATAGT
461361 AAACTATTCT
Statistics
Matches: 81, Mismatches: 10, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
14 9 0.11
16 2 0.02
17 2 0.02
18 2 0.02
20 66 0.81
ACGTcount: A:0.21, C:0.18, G:0.19, T:0.42
Consensus pattern (20 bp):
ATAGTCATTTTCGCATTACG
Found at i:461305 original size:74 final size:74
Alignment explanation
Indices: 461216--461360 Score: 211
Period size: 74 Copynumber: 2.0 Consensus size: 74
461206 GCAATTTTCA
* * *
461216 TTTCGCATTACGATTCTTTCGTTGCAATAGTCATTTTCGTATT-ACGATAGTCATTTTCGCATTG
1 TTTCGCATTACGATTCTCTCATTGCAATAGTCATTTTCGCATTGA-GATAGTCATTTTCGCATTG
461280 CGATAGTCAT
65 CGATAGTCAT
** * *
461290 TTTCGCATTGTGATTCTCTCATTGCGATAGTCATTTTCGCGTTGAGATAGTCATTTTCGCATTGC
1 TTTCGCATTACGATTCTCTCATTGCAATAGTCATTTTCGCATTGAGATAGTCATTTTCGCATTGC
461355 GATAGT
66 GATAGT
461361 AAACTATTCT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
74 62 0.98
75 1 0.02
ACGTcount: A:0.20, C:0.19, G:0.19, T:0.43
Consensus pattern (74 bp):
TTTCGCATTACGATTCTCTCATTGCAATAGTCATTTTCGCATTGAGATAGTCATTTTCGCATTGC
GATAGTCAT
Found at i:463278 original size:20 final size:20
Alignment explanation
Indices: 463235--463302 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
463225 GAAACTTTAA
* * **
463235 ATCGCAACATGAAAATAAAA
1 ATCGCAACACGAAAATGACT
463255 ATCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGACT
* **
463275 ATCGCAACGCGAATTTGACT
1 ATCGCAACACGAAAATGACT
463295 ATCGCAAC
1 ATCGCAAC
463303 GCAAGAATCG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.44, C:0.24, G:0.15, T:0.18
Consensus pattern (20 bp):
ATCGCAACACGAAAATGACT
Found at i:463373 original size:20 final size:20
Alignment explanation
Indices: 463348--463394 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
463338 GATTCTCTCG
463348 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
463368 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
463388 TTGCGAT
1 TTGCGAT
463395 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:464008 original size:20 final size:20
Alignment explanation
Indices: 463963--464052 Score: 74
Period size: 20 Copynumber: 4.5 Consensus size: 20
463953 GCGCTATGTA
* *
463963 AATCGCATTGCGATAGT-CAT
1 AATCGCATTGCGAT-TTACGT
*
463983 ATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACGT
* **
464003 AATCGCATTGCGATTTTCCA
1 AATCGCATTGCGATTTACGT
* *
464023 AATTCGCGTTGTGATTTACGT
1 AA-TCGCATTGCGATTTACGT
*
464044 ATTCGCATT
1 AATCGCATT
464053 ACGAATTAGG
Statistics
Matches: 54, Mismatches: 14, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
19 1 0.02
20 39 0.72
21 14 0.26
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (20 bp):
AATCGCATTGCGATTTACGT
Found at i:464040 original size:41 final size:40
Alignment explanation
Indices: 463963--464052 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 40
463953 GCGCTATGTA
*
463963 AATCGCATTGCGATAGTCATATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGT
** * *
464003 AATCGCATTGCGATTTTCCAAATTCGCGTTGTGATTTACGT
1 AATCGCATTGCGATAGT-CAAATTCGCATTGCGATTTACGT
*
464044 ATTCGCATT
1 AATCGCATT
464053 ACGAATTAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 15 0.35
41 28 0.65
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (40 bp):
AATCGCATTGCGATAGTCAAATTCGCATTGCGATTTACGT
Found at i:464078 original size:21 final size:21
Alignment explanation
Indices: 464054--464098 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
464044 ATTCGCATTA
464054 CGAATTAGGAAAATCGCAACG
1 CGAATTAGGAAAATCGCAACG
* * *
464075 CGAATTTGGGAAATCGCAATG
1 CGAATTAGGAAAATCGCAACG
464096 CGA
1 CGA
464099 TAGTTAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.18, G:0.27, T:0.18
Consensus pattern (21 bp):
CGAATTAGGAAAATCGCAACG
Found at i:469598 original size:187 final size:187
Alignment explanation
Indices: 469283--469657 Score: 750
Period size: 187 Copynumber: 2.0 Consensus size: 187
469273 TTGAAGGCTA
469283 GACTGAGCAAAAACCTACAGAGTATCATGGCTAGGAACAGTGAGAACAAGTCGACGACGAGTAGA
1 GACTGAGCAAAAACCTACAGAGTATCATGGCTAGGAACAGTGAGAACAAGTCGACGACGAGTAGA
469348 GTGAGTGACCACTTCACTTTCGCTAATATATTCCACTTTAGAAAACATCAGTACCGGGACACGGC
66 GTGAGTGACCACTTCACTTTCGCTAATATATTCCACTTTAGAAAACATCAGTACCGGGACACGGC
469413 TGTTGATATGAAGAATATTCAAAGAGTGGTGCAACCGAGCATCATTGTGCCACACGT
131 TGTTGATATGAAGAATATTCAAAGAGTGGTGCAACCGAGCATCATTGTGCCACACGT
469470 GACTGAGCAAAAACCTACAGAGTATCATGGCTAGGAACAGTGAGAACAAGTCGACGACGAGTAGA
1 GACTGAGCAAAAACCTACAGAGTATCATGGCTAGGAACAGTGAGAACAAGTCGACGACGAGTAGA
469535 GTGAGTGACCACTTCACTTTCGCTAATATATTCCACTTTAGAAAACATCAGTACCGGGACACGGC
66 GTGAGTGACCACTTCACTTTCGCTAATATATTCCACTTTAGAAAACATCAGTACCGGGACACGGC
469600 TGTTGATATGAAGAATATTCAAAGAGTGGTGCAACCGAGCATCATTGTGCCACACGT
131 TGTTGATATGAAGAATATTCAAAGAGTGGTGCAACCGAGCATCATTGTGCCACACGT
469657 G
1 G
469658 GGTGATGTGC
Statistics
Matches: 188, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
187 188 1.00
ACGTcount: A:0.34, C:0.21, G:0.24, T:0.22
Consensus pattern (187 bp):
GACTGAGCAAAAACCTACAGAGTATCATGGCTAGGAACAGTGAGAACAAGTCGACGACGAGTAGA
GTGAGTGACCACTTCACTTTCGCTAATATATTCCACTTTAGAAAACATCAGTACCGGGACACGGC
TGTTGATATGAAGAATATTCAAAGAGTGGTGCAACCGAGCATCATTGTGCCACACGT
Found at i:475869 original size:35 final size:35
Alignment explanation
Indices: 475823--475898 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
475813 AAAACAGTCC
* *
475823 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
475858 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
475893 TCAATT
1 TCAATT
475899 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:476443 original size:130 final size:130
Alignment explanation
Indices: 476297--476544 Score: 406
Period size: 130 Copynumber: 1.9 Consensus size: 130
476287 TATTTATATA
* **
476297 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
476362 TTAGCACATGATCATAACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATAACACATGTCATCGGTGACACATGTCACCACCTAATTATTTATATATGCT
476427 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * * *
476492 TTAACACATGATCATGATATATGTTATCGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATAACACATGTCATCGGTGACACATGTCACCACCTAATTA
476545 GAAGAAAATT
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 108 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATAACACATGTCATCGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:476575 original size:130 final size:129
Alignment explanation
Indices: 476311--476575 Score: 291
Period size: 130 Copynumber: 2.0 Consensus size: 129
476301 ATTTGGTCCT
* ** *
476311 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * *** * * **** *
476376 TAACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TAACACATGTCATCGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
476441 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * * *
476506 TGATATATGTTATCGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TAACACATGTCATCGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
476570 -A
128 CA
476571 AAATT
1 AAATT
476576 TGGGTCTTGG
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
130 98 0.88
132 8 0.07
133 5 0.05
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TAACACATGTCATCGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:483687 original size:25 final size:25
Alignment explanation
Indices: 483642--483689 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
483632 AAAATCCCCT
**
483642 CAAAAAACCTACTCCAGGACCTCCA
1 CAAAAAACCTACGACAGGACCTCCA
483667 CAAAAAACC-ACGACAGAGACCTC
1 CAAAAAACCTACGACAG-GACCTC
483690 AAATTCCAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.44, C:0.38, G:0.10, T:0.08
Consensus pattern (25 bp):
CAAAAAACCTACGACAGGACCTCCA
Found at i:484506 original size:2 final size:2
Alignment explanation
Indices: 484501--484537 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
484491 GTGTGTGTGT
*
484501 GA GA GA GA GA GA GA GA G- GG GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
484538 ACTTTAATGA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:485915 original size:2 final size:2
Alignment explanation
Indices: 485910--485934 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
485900 CGGAGAGGGG
485910 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
485935 GGAAGCAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:493669 original size:3 final size:3
Alignment explanation
Indices: 493661--493686 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
493651 ATTTTCATTT
493661 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
493687 ATGAAACCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:496345 original size:60 final size:60
Alignment explanation
Indices: 496273--496387 Score: 169
Period size: 60 Copynumber: 1.9 Consensus size: 60
496263 GAATAGTCGA
* * *
496273 GGGACCATTTTGTAACTTTTAATAGTCGA-GAGACTTAATAAAGTATTATCCTATAATCAG
1 GGGACCATTTTGTAACTTTTAATAGTCAATGA-ACTCAATAAAGCATTATCCTATAATCAG
* *
496333 GGGACCATTTTGTATCTTTTAATAGTTAATGAACTCAATAAAGCATTATCCTATA
1 GGGACCATTTTGTAACTTTTAATAGTCAATGAACTCAATAAAGCATTATCCTATA
496388 GTCGGAGGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
60 47 0.96
61 2 0.04
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (60 bp):
GGGACCATTTTGTAACTTTTAATAGTCAATGAACTCAATAAAGCATTATCCTATAATCAG
Found at i:496402 original size:60 final size:60
Alignment explanation
Indices: 496265--496408 Score: 168
Period size: 60 Copynumber: 2.4 Consensus size: 60
496255 AACATAATGA
* * * *
496265 ATAGTC-GAGGGACCATTTTGTAACTTTTAATAGTCGAGAGACTTAATAAAGTATTATCCT
1 ATAGTCGGA-GGACCATTTTGTATCTTTTAATAGTCAAGAGACTCAATAAAGCATTATCCT
* *
496325 ATAATCAGG-GGACCATTTTGTATCTTTTAATAGTTAATGA-ACTCAATAAAGCATTATCCT
1 ATAGTC-GGAGGACCATTTTGTATCTTTTAATAGTCAA-GAGACTCAATAAAGCATTATCCT
*
496385 ATAGTCGGAGGATCATTTGTGTAT
1 ATAGTCGGAGGACCATTT-TGTAT
496409 TTTACTCTTT
Statistics
Matches: 71, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
59 2 0.03
60 61 0.86
61 7 0.10
62 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (60 bp):
ATAGTCGGAGGACCATTTTGTATCTTTTAATAGTCAAGAGACTCAATAAAGCATTATCCT
Found at i:498688 original size:23 final size:23
Alignment explanation
Indices: 498632--498695 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
498622 TTTTTGTGAC
* * *
498632 ACATTCATCTATGCCTTTATGAC
1 ACATTTATCTTTGCCTTTATGAA
*
498655 ACATTTATCTTTGTCTTTATGAA
1 ACATTTATCTTTGCCTTTATGAA
* *
498678 ACGTTTTTCTTTGCCTTT
1 ACATTTATCTTTGCCTTT
498696 TGGTAGTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.20, G:0.09, T:0.50
Consensus pattern (23 bp):
ACATTTATCTTTGCCTTTATGAA
Found at i:502818 original size:17 final size:17
Alignment explanation
Indices: 502796--502828 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
502786 GCCAAGGTGA
502796 GTGCATATTATTAGATT
1 GTGCATATTATTAGATT
502813 GTGCATATTATTAGAT
1 GTGCATATTATTAGAT
502829 GGGAATTAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.18, T:0.45
Consensus pattern (17 bp):
GTGCATATTATTAGATT
Found at i:504185 original size:23 final size:24
Alignment explanation
Indices: 504132--504192 Score: 81
Period size: 23 Copynumber: 2.6 Consensus size: 24
504122 ACATTTTATA
*
504132 TGGCACTTCGGTGCAATTCTTCGC
1 TGGCACTTCGGTGCAATTCTACGC
*
504156 T-GTACTTCGGTGCAATTCTACG-
1 TGGCACTTCGGTGCAATTCTACGC
*
504178 TGGCACTTAGGTGCA
1 TGGCACTTCGGTGCA
504193 TTTATACGAG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 1 0.03
23 30 0.94
24 1 0.03
ACGTcount: A:0.16, C:0.25, G:0.26, T:0.33
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTCTACGC
Found at i:508567 original size:23 final size:23
Alignment explanation
Indices: 508537--508590 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
508527 ACATTTTATA
*
508537 TGGCACTTCGGTTCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
508560 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
508583 TGGCACTT
1 TGGCACTT
508591 ATGTGCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:508596 original size:23 final size:23
Alignment explanation
Indices: 508537--508597 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
508527 ACATTTTATA
* *
508537 TGGCACTTCGGTTCAATTCTACG
1 TGGCACTTAGGTGCAATTCTACG
*
508560 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTAGGTGCAATTCTACG
*
508583 TGGCACTTATGTGCA
1 TGGCACTTAGGTGCA
508598 TTTATACGAG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.33
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:508605 original size:23 final size:23
Alignment explanation
Indices: 508537--508605 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
508527 ACATTTTATA
* * *
508537 TGGCACTTCGGTTCAATTCTACG
1 TGGCACTTAGGTGCAATTATACG
* *
508560 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTAGGTGCAATTATACG
* *
508583 TGGCACTTATGTGCATTTATACG
1 TGGCACTTAGGTGCAATTATACG
508606 AGTTGTGGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.19, C:0.23, G:0.23, T:0.35
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTATACG
Found at i:511675 original size:37 final size:37
Alignment explanation
Indices: 511625--511700 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
511615 TTAGTGCACG
511625 TGGCTGAATGTGATTCGTGTTCCAATGTGGGCGAAAA
1 TGGCTGAATGTGATTCGTGTTCCAATGTGGGCGAAAA
511662 TGGCTGAATGTGATTCGTGTTCCAATGTGGGCGAAAA
1 TGGCTGAATGTGATTCGTGTTCCAATGTGGGCGAAAA
511699 TG
1 TG
511701 ATTCGTGCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.24, C:0.13, G:0.33, T:0.30
Consensus pattern (37 bp):
TGGCTGAATGTGATTCGTGTTCCAATGTGGGCGAAAA
Found at i:514574 original size:20 final size:20
Alignment explanation
Indices: 514549--514595 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
514539 TTTTTCAAAT
*
514549 TCGCAACGTGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
* * *
514569 TCGCAATGCGGATTTGTAAA
1 TCGCAACGCGAATCTGTAAA
514589 TCGCAAC
1 TCGCAAC
514596 ACAGAAGTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:514612 original size:20 final size:20
Alignment explanation
Indices: 514589--514635 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
514579 GATTTGTAAA
*
514589 TCGCAACACAGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
514609 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
514629 TCGCAAC
1 TCGCAAC
514636 GTGAATAGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.45, C:0.28, G:0.13, T:0.15
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:514652 original size:20 final size:20
Alignment explanation
Indices: 514629--514676 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
514619 AAAGTCAAAT
514629 TCGCAACGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
*
514649 TCGCAATGTGAATAGTAAAA
1 TCGCAACGTGAATAGTAAAA
514669 TCGCAACG
1 TCGCAACG
514677 AATCTATATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAACGTGAATAGTAAAA
Found at i:515081 original size:20 final size:20
Alignment explanation
Indices: 515053--515107 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
515043 CGCGTTACGA
515053 TCACGTTACGATTTTACTAT
1 TCACGTTACGATTTTACTAT
*
515073 TCGCGTTACGATTTTACTAT
1 TCACGTTACGATTTTACTAT
* *
515093 TTACGCTACGATTTT
1 TCACGTTACGATTTT
515108 GGAAACTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.45
Consensus pattern (20 bp):
TCACGTTACGATTTTACTAT
Found at i:515256 original size:14 final size:14
Alignment explanation
Indices: 515237--515263 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
515227 TCTTATTTTT
515237 TTATATTTTTTTAA
1 TTATATTTTTTTAA
515251 TTATATTTTTTTA
1 TTATATTTTTTTA
515264 CTAGTACTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (14 bp):
TTATATTTTTTTAA
Found at i:520762 original size:10 final size:10
Alignment explanation
Indices: 520739--520782 Score: 56
Period size: 9 Copynumber: 4.6 Consensus size: 10
520729 ACATACTATT
520739 TTTTTTGT-A
1 TTTTTTGTGA
* *
520748 ATTTTTCTGA
1 TTTTTTGTGA
520758 TTTTTTGT-A
1 TTTTTTGTGA
520767 TTTTTTGTGA
1 TTTTTTGTGA
520777 TTTTTT
1 TTTTTT
520783 AAAATTCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
9 15 0.52
10 14 0.48
ACGTcount: A:0.11, C:0.02, G:0.11, T:0.75
Consensus pattern (10 bp):
TTTTTTGTGA
Found at i:520763 original size:19 final size:19
Alignment explanation
Indices: 520739--520782 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
520729 ACATACTATT
520739 TTTTTTGTAATTTTTCTGA
1 TTTTTTGTAATTTTTCTGA
* *
520758 TTTTTTGTATTTTTTGTGA
1 TTTTTTGTAATTTTTCTGA
520777 TTTTTT
1 TTTTTT
520783 AAAATTCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.02, G:0.11, T:0.75
Consensus pattern (19 bp):
TTTTTTGTAATTTTTCTGA
Found at i:520797 original size:113 final size:114
Alignment explanation
Indices: 520664--520911 Score: 401
Period size: 114 Copynumber: 2.2 Consensus size: 114
520654 CATTTCCTTT
* * *
520664 TTTTTTTAAATT-AAATTAGATTAAATTATAATATAAATAAAAATACATTGAAATTAGATATATA
1 TTTTTTTAAATTCAAA-TAGATTAAATTACAAGATAAATAAAAATACATTGAAATTAGATAAATA
*
520728 AACATACT-ATTTTTTTTGTAATTTTTCTGATTTTTTGTATTTTTTGTGA
65 AACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTGTATTTTTTCTGA
* * * *
520777 TTTTTTAAAATTCAAATAGATTAATTTGCAAGATAGATAAAAATACATTGAAATTAGATAAATAA
1 TTTTTTTAAATTCAAATAGATTAAATTACAAGATAAATAAAAATACATTGAAATTAGATAAATAA
520842 ACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTGTATTTTTTCTGA
66 ACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTGTATTTTTTCTGA
520891 TTTTTTTAAATTCAAATAGAT
1 TTTTTTTAAATTCAAATAGAT
520912 ATTTATTAGA
Statistics
Matches: 124, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
113 61 0.49
114 63 0.51
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.50
Consensus pattern (114 bp):
TTTTTTTAAATTCAAATAGATTAAATTACAAGATAAATAAAAATACATTGAAATTAGATAAATAA
ACATACTAATTTTTTTTGTAATTTTTCTGATTTTTTGTATTTTTTCTGA
Found at i:520876 original size:10 final size:10
Alignment explanation
Indices: 520863--520896 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
520853 TTTTTTGTAA
520863 TTTTTCTGAT
1 TTTTTCTGAT
*
520873 TTTTTGT-AT
1 TTTTTCTGAT
520882 TTTTTCTGAT
1 TTTTTCTGAT
520892 TTTTT
1 TTTTT
520897 TAAATTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
9 8 0.38
10 13 0.62
ACGTcount: A:0.09, C:0.06, G:0.09, T:0.76
Consensus pattern (10 bp):
TTTTTCTGAT
Found at i:520877 original size:19 final size:19
Alignment explanation
Indices: 520853--520896 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
520843 CATACTAATT
520853 TTTTTTGTAATTTTTCTGA
1 TTTTTTGTAATTTTTCTGA
*
520872 TTTTTTGTATTTTTTCTGA
1 TTTTTTGTAATTTTTCTGA
520891 TTTTTT
1 TTTTTT
520897 TAAATTCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.11, C:0.05, G:0.09, T:0.75
Consensus pattern (19 bp):
TTTTTTGTAATTTTTCTGA
Found at i:521331 original size:42 final size:42
Alignment explanation
Indices: 521251--521332 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
521241 TGGTTCCCGA
* *
521251 GTTGGAGTGTTCTGCTGCTATCGAAGTTCATGCACACAATGT
1 GTTGGAGGGTTCTGCTGCTATCGAAGTTAATGCACACAATGT
* * *
521293 GTTGGAGGGTTGTGCTGCTCTCGATAG-TAATGCGCACAAT
1 GTTGGAGGGTTCTGCTGCTATCGA-AGTTAATGCACACAAT
521333 AAGTCTATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 32 0.94
43 2 0.06
ACGTcount: A:0.21, C:0.18, G:0.29, T:0.32
Consensus pattern (42 bp):
GTTGGAGGGTTCTGCTGCTATCGAAGTTAATGCACACAATGT
Found at i:545182 original size:26 final size:27
Alignment explanation
Indices: 545127--545204 Score: 85
Period size: 26 Copynumber: 3.0 Consensus size: 27
545117 ATTTGATTTT
* *
545127 AATTTTAATATCAATTTTTTAA-A-TA
1 AATTATAATATTAATTTTTTAATATTA
545152 AATTA-AATATTAATTTTTTAATATTA
1 AATTATAATATTAATTTTTTAATATTA
*
545178 TATTATAGATATTAA--TTTTAATATTA
1 AATTATA-ATATTAATTTTTTAATATTA
545204 A
1 A
545205 TTTTTAAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
24 15 0.33
25 5 0.11
26 17 0.38
27 1 0.02
28 7 0.16
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (27 bp):
AATTATAATATTAATTTTTTAATATTA
Found at i:545205 original size:40 final size:36
Alignment explanation
Indices: 545157--545239 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 36
545147 AAATAAATTA
*
545157 AATATTAATTTTTTAATATTATATTATAGATATTAA-TTTT
1 AATATTAA-TTTTTAA-A-TAAATTA-A-ATATTAATTTTT
545197 AATATTAATTTTTAAATAAATTAAATATTAATTTTT
1 AATATTAATTTTTAAATAAATTAAATATTAATTTTT
545233 AATATTA
1 AATATTA
545240 TATTATAGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
35 7 0.17
36 12 0.29
37 6 0.15
38 1 0.02
39 7 0.17
40 8 0.20
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (36 bp):
AATATTAATTTTTAAATAAATTAAATATTAATTTTT
Found at i:545237 original size:62 final size:63
Alignment explanation
Indices: 545102--545265 Score: 250
Period size: 62 Copynumber: 2.7 Consensus size: 63
545092 GGTTTTATAT
*
545102 TTAA-TTTT-ATATTATATT-T-GATTTTAATTTTAATATCAATTTTTTAAATAAATTAAATA
1 TTAATTTTTAATATTATATTATAGATATTAATTTTAATATCAATTTTTTAAATAAATTAAATA
*
545161 TTAATTTTTTAATATTATATTATAGATATTAATTTTAATATTAA-TTTTTAAATAAATTAAATA
1 TTAA-TTTTTAATATTATATTATAGATATTAATTTTAATATCAATTTTTTAAATAAATTAAATA
545224 TTAATTTTTAATATTATATTATAGATATTTAATTTT-ATATCA
1 TTAATTTTTAATATTATATTATAGATA-TTAATTTTAATATCA
545266 TATAAATTAT
Statistics
Matches: 96, Mismatches: 3, Indels: 9
0.89 0.03 0.08
Matches are distributed among these distances:
59 4 0.04
61 4 0.04
62 38 0.40
63 32 0.33
64 18 0.19
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (63 bp):
TTAATTTTTAATATTATATTATAGATATTAATTTTAATATCAATTTTTTAAATAAATTAAATA
Done.