Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008999.1 Hibiscus syriacus cultivar Beakdansim tig00112380_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: 605736
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:340637 original size:22 final size:22
Alignment explanation
Indices: 340610--340671 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
340600 TTCTTTTCCC
*
340610 AGTGTTAAGACACTTTTGTATT
1 AGTGTTAAGGCACTTTTGTATT
* * *
340632 GGTGTTGAGGCACTTTAGTATT
1 AGTGTTAAGGCACTTTTGTATT
*
340654 AGTGCTAAGGCACTTTTG
1 AGTGTTAAGGCACTTTTG
340672 AAATTTAATG
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (22 bp):
AGTGTTAAGGCACTTTTGTATT
Found at i:342568 original size:23 final size:23
Alignment explanation
Indices: 342542--342585 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
342532 AAAATATTCA
*
342542 AAAATCATGAAACCCTAATAATG
1 AAAACCATGAAACCCTAATAATG
*
342565 AAAACCATGAAATCCTAATAA
1 AAAACCATGAAACCCTAATAA
342586 AACCAAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.55, C:0.18, G:0.07, T:0.20
Consensus pattern (23 bp):
AAAACCATGAAACCCTAATAATG
Found at i:347025 original size:6 final size:6
Alignment explanation
Indices: 347009--347039 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
346999 TATTATGTTA
347009 TTATATT TTATTT TTATTT TTATTT TTATTT
1 TTAT-TT TTATTT TTATTT TTATTT TTATTT
347040 GCTCCTTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTATTT
Found at i:347025 original size:13 final size:13
Alignment explanation
Indices: 346991--347037 Score: 60
Period size: 12 Copynumber: 3.5 Consensus size: 13
346981 CCTTACTTAT
*
346991 TTTTTATATATTA
1 TTTTTATATTTTA
347004 TGTTATTATATTTTA
1 T-TT-TTATATTTTA
347019 TTTTTAT-TTTTA
1 TTTTTATATTTTA
347031 TTTTTAT
1 TTTTTAT
347038 TTGCTCCTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 12 0.39
13 5 0.16
14 4 0.13
15 10 0.32
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (13 bp):
TTTTTATATTTTA
Found at i:347317 original size:9 final size:9
Alignment explanation
Indices: 347303--347335 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
347293 AATATCTTAG
347303 TTTAATTCA
1 TTTAATTCA
*
347312 TTTAATTCG
1 TTTAATTCA
347321 TTTAATT-A
1 TTTAATTCA
347329 TTTAATT
1 TTTAATT
347336 TTTTTATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 7 0.32
9 15 0.68
ACGTcount: A:0.30, C:0.06, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTAATTCA
Found at i:347341 original size:17 final size:18
Alignment explanation
Indices: 347302--347335 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
347292 TAATATCTTA
347302 GTTTAATTCATTTAATTC
1 GTTTAATTCATTTAATTC
347320 GTTTAATT-ATTTAATT
1 GTTTAATTCATTTAATT
347336 TTTTTATTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (18 bp):
GTTTAATTCATTTAATTC
Found at i:348182 original size:20 final size:21
Alignment explanation
Indices: 348159--348201 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
348149 GACCAAAAAG
* *
348159 TTATTATAATAATTAAA-ATT
1 TTATTAAAATAATAAAACATT
348179 TTATTAAAATAATAAAACATT
1 TTATTAAAATAATAAAACATT
348200 TT
1 TT
348202 TTTAGTGATC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATTAAAATAATAAAACATT
Found at i:349732 original size:11 final size:11
Alignment explanation
Indices: 349697--349737 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
349687 AAGTATTGAC
*
349697 TTTATTTATGA
1 TTTATTTATAA
349708 TTT-TTTAT-A
1 TTTATTTATAA
349717 TTTATTTATAA
1 TTTATTTATAA
*
349728 TTTATATATA
1 TTTATTTATA
349738 TATCATACCA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 4 0.15
10 10 0.37
11 13 0.48
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (11 bp):
TTTATTTATAA
Found at i:350122 original size:21 final size:20
Alignment explanation
Indices: 350096--350193 Score: 79
Period size: 21 Copynumber: 4.8 Consensus size: 20
350086 ATCAGTTTCC
350096 AAAATCGCAACGCGATTCTTA
1 AAAATCGCAACGCGATT-TTA
* **
350117 AAAATCGCAATGCGATAGTA
1 AAAATCGCAACGCGATTTTA
* ** *
350137 CAAATTCGCATTGCGATTTTCC
1 -AAAATCGCAACGCGATTTT-A
* * *
350159 AAAATCGCAACGCGAATATG
1 AAAATCGCAACGCGATTTTA
350179 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
350194 ACACATAAAT
Statistics
Matches: 61, Mismatches: 14, Indels: 5
0.76 0.17 0.06
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTTA
Found at i:350222 original size:20 final size:20
Alignment explanation
Indices: 350160--350389 Score: 232
Period size: 20 Copynumber: 11.5 Consensus size: 20
350150 CGATTTTCCA
* ** *
350160 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
350180 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
350200 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
350220 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
350240 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
350260 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
350280 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
350300 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
350320 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
350340 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
350360 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
350380 AAATCACAAC
1 AAATCGCAAC
350390 ACTGAAATTT
Statistics
Matches: 176, Mismatches: 28, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 172 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:351097 original size:24 final size:24
Alignment explanation
Indices: 351070--351116 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
351060 AAATTTGGTC
351070 TTGGTCAATATC-CGGACTTTGATA
1 TTGGTCAATA-CACGGACTTTGATA
*
351094 TTGGTCAATACACGGATTTTGAT
1 TTGGTCAATACACGGACTTTGAT
351117 GATGTTTTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATACACGGACTTTGATA
Found at i:353648 original size:33 final size:34
Alignment explanation
Indices: 353597--353807 Score: 224
Period size: 33 Copynumber: 6.2 Consensus size: 34
353587 CGGAAATTAC
*
353597 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
353630 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGC-GAAATGAA
*
353664 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
*
353697 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
353730 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--ATGAAAATCGCAATGCGAAATGAA
* *
353768 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACGATGAAAATCGCAATGCGAAATGAA
353801 AATCGCA
1 AATCGCA
353808 TTGCGATTCT
Statistics
Matches: 156, Mismatches: 9, Indels: 26
0.82 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 93 0.60
34 31 0.20
35 5 0.03
36 4 0.03
37 2 0.01
38 20 0.13
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACGATGAAAATCGCAATGCGAAATGAA
Found at i:353702 original size:19 final size:19
Alignment explanation
Indices: 353611--353813 Score: 203
Period size: 19 Copynumber: 11.7 Consensus size: 19
353601 GCAACGAGAG
353611 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
353630 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
353644 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
353664 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
353678 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
353697 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
353716 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
353730 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
353749 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
353768 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
353782 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
353801 AATCGCATTGCGA
1 AATCGCAATGCGA
353814 TTCTCTCGTT
Statistics
Matches: 153, Mismatches: 10, Indels: 42
0.75 0.05 0.20
Matches are distributed among these distances:
14 42 0.27
15 3 0.02
16 7 0.05
17 6 0.04
18 4 0.03
19 78 0.51
20 13 0.08
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:353724 original size:52 final size:52
Alignment explanation
Indices: 353639--353813 Score: 323
Period size: 52 Copynumber: 3.3 Consensus size: 52
353629 AAATCCCAAC
353639 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
353692 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
353744 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* *
353796 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
353814 TTCTCTCGTT
Statistics
Matches: 120, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
52 104 0.87
53 16 0.13
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:353861 original size:53 final size:52
Alignment explanation
Indices: 353803--353919 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 52
353793 GAAATTAAAA
353803 TCGCATTGCGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCAT-TCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
353856 TCGCATTGCGATTCATTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCATTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
*
353908 TCACATTGCGAT
1 TCGCATTGCGAT
353920 AGTCATTTTT
Statistics
Matches: 62, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
52 29 0.47
53 32 0.52
54 1 0.02
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTCATTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
Found at i:353862 original size:19 final size:19
Alignment explanation
Indices: 353822--353919 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
353812 GATTCTCTCG
353822 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
353842 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
353861 TTGCGA--TTCA-TTCG--
1 TTGCGATTTTCATTTCGCA
353875 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
353894 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCA
353913 TTGCGAT
1 TTGCGAT
353920 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 1, Indels: 11
0.86 0.01 0.13
Matches are distributed among these distances:
14 6 0.08
16 8 0.11
17 8 0.11
19 35 0.49
20 15 0.21
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:353916 original size:52 final size:53
Alignment explanation
Indices: 353806--353919 Score: 196
Period size: 52 Copynumber: 2.2 Consensus size: 53
353796 ATTAAAATCG
*
353806 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1 CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCA
353859 CATTGCGATTCAT-TCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCA
1 CATTGCGATTC-TCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCA
353911 CATTGCGAT
1 CATTGCGAT
353920 AGTCATTTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 3
0.94 0.02 0.05
Matches are distributed among these distances:
52 29 0.49
53 29 0.49
54 1 0.02
ACGTcount: A:0.16, C:0.23, G:0.17, T:0.45
Consensus pattern (53 bp):
CATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCA
Found at i:353925 original size:19 final size:19
Alignment explanation
Indices: 353884--353927 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
353874 GTTGCGATTT
* **
353884 TCATTTCGCATTGCGATTT
1 TCATTTCACATTGCGATAG
353903 TCATTTCACATTGCGATAG
1 TCATTTCACATTGCGATAG
353922 TCATTT
1 TCATTT
353928 TTGCCTTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.45
Consensus pattern (19 bp):
TCATTTCACATTGCGATAG
Found at i:354045 original size:14 final size:14
Alignment explanation
Indices: 354026--354062 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
354016 CATCAATTAC
354026 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
354040 ACAAATCATCTTTT
1 ACAAATCAACTTTT
354054 ACAAATCAA
1 ACAAATCAA
354063 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:356031 original size:19 final size:19
Alignment explanation
Indices: 355989--356161 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
355979 TAGTTTACTT
* *
355989 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
356009 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
356028 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
356047 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
356066 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
356085 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
356099 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
356118 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
356132 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
356151 TCGCAATGCGA
1 TCGCAACGCGA
356162 TTTTGGTTTC
Statistics
Matches: 130, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
14 16 0.12
16 11 0.08
17 11 0.08
19 80 0.62
20 12 0.09
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:356102 original size:14 final size:14
Alignment explanation
Indices: 356083--356139 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
356073 GCGAAATGAA
*
356083 AATCGCAACGACAG
1 AATCGCAACGAAAG
356097 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
356114 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
356130 AATCGCAACG
1 AATCGCAACG
356140 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:356110 original size:33 final size:33
Alignment explanation
Indices: 356064--356156 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
356054 GCGAAACCAA
*
356064 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
356097 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
356130 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
356157 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:356179 original size:19 final size:19
Alignment explanation
Indices: 356157--356285 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
356147 AAAATCGCAA
356157 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
356176 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
*
356190 TGTGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
356209 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
356223 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
356242 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
356261 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
356281 TGCGA
1 TGCGA
356286 AAGTAACCTA
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 21 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 47 0.53
20 13 0.15
ACGTcount: A:0.09, C:0.16, G:0.29, T:0.47
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:356202 original size:33 final size:33
Alignment explanation
Indices: 356157--356248 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
356147 AAAATCGCAA
356157 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
*
356190 TGTGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
356223 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
356249 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 52 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:356449 original size:93 final size:93
Alignment explanation
Indices: 356333--356708 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
356323 ATGGATTGCA
356333 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
356397 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
356425 TTACTTTCAACCAAAAGACAAAACAAAGACCAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
356490 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
356518 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
356583 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
356611 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
356676 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
356704 TTACT
1 TTACT
356709 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 276 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:358439 original size:20 final size:20
Alignment explanation
Indices: 358408--358504 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
358398 TTTTGGTTGA
358408 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
358428 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
358448 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
358467 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
358482 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
358502 AAT
1 AAT
358505 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:358460 original size:21 final size:21
Alignment explanation
Indices: 358406--358470 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
358396 TCTTTTGGTT
358406 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
358427 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
358447 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
358468 GAA
1 GAA
358471 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:358474 original size:14 final size:14
Alignment explanation
Indices: 358455--358511 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
358445 GAGAAATGAA
358455 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
358469 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
358488 AATCGCAACGAGAG
1 AATCGCAACGAGAG
358502 AATCGCAACG
1 AATCGCAACG
358512 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:358487 original size:33 final size:33
Alignment explanation
Indices: 358406--358528 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
358396 TCTTTTGGTT
*
358406 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
358447 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
358480 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
358513 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
358529 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:358628 original size:41 final size:41
Alignment explanation
Indices: 358571--358648 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
358561 TCGCGTTGCG
*
358571 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
358612 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
358649 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:358633 original size:20 final size:21
Alignment explanation
Indices: 358572--358647 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
358562 CGCGTTGCGA
358572 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
358593 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
358613 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
358634 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
358648 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:358769 original size:33 final size:33
Alignment explanation
Indices: 358727--358797 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
358717 AATACTAACT
*
358727 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
358760 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
358793 TGAAA
1 TGAAA
358798 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:359031 original size:22 final size:22
Alignment explanation
Indices: 358979--359033 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
358969 TGGTTGTGAG
**
358979 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
359001 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
359023 GGATTTCTTCG
1 GGATTTCTTCG
359034 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:359209 original size:20 final size:20
Alignment explanation
Indices: 359180--359353 Score: 215
Period size: 20 Copynumber: 8.7 Consensus size: 20
359170 CTTTAAATAT
359180 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
359200 CGCATTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
359222 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
359241 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
359261 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
359281 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
359301 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
359321 CGCGTTGCGATTTATGTATT
1 CGCGTTGCGATTTACGGATA
359341 CGCGTTGCGATTT
1 CGCGTTGCGATTT
359354 TGGAAAATCG
Statistics
Matches: 130, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
19 2 0.02
20 113 0.87
21 13 0.10
22 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:359317 original size:60 final size:60
Alignment explanation
Indices: 359182--359353 Score: 247
Period size: 60 Copynumber: 2.9 Consensus size: 60
359172 TTAAATATCG
* *
359182 CGTTGCGATTTACGGATACGCATTGCGATTTTATGTATTA-TCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTATGTA-TACGCGTTGCGATTTACGGATACA
* ***
359243 CGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATACGCGTTGCGATTTACGGATACA
* *
359303 CGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTT
1 CGTTGCGATTTACGGATACGCATTGCGATTTATGTATACGCGTTGCGATTT
359354 TGGAAAATCG
Statistics
Matches: 98, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
59 2 0.02
60 69 0.70
61 27 0.28
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTATGTATACGCGTTGCGATTTACGGATACA
Found at i:359370 original size:21 final size:21
Alignment explanation
Indices: 359340--359422 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
359330 ATTTATGTAT
*
359340 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
359361 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
359382 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
359403 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
359423 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:359413 original size:42 final size:40
Alignment explanation
Indices: 359321--359418 Score: 108
Period size: 42 Copynumber: 2.4 Consensus size: 40
359311 TTTACGGATA
* *
359321 CGCGTTGCGATTTATGTATTCGCGTTGCGATTTTGGAAAAT
1 CGCGTTGCGATTT-TGTATTCGCATTGCGATTTTGCAAAAT
** *
359362 CGCAATGCGAATTTGTACTATCGCATTGCGATTTT-CAAGAAT
1 CGCGTTGCGATTTTGTA-T-TCGCATTGCGATTTTGCAA-AAT
359404 CGCGTTGCGATTTTG
1 CGCGTTGCGATTTTG
359419 GAAACTGATT
Statistics
Matches: 46, Mismatches: 8, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
40 4 0.09
41 13 0.28
42 29 0.63
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.37
Consensus pattern (40 bp):
CGCGTTGCGATTTTGTATTCGCATTGCGATTTTGCAAAAT
Found at i:361271 original size:211 final size:208
Alignment explanation
Indices: 360901--361399 Score: 718
Period size: 211 Copynumber: 2.4 Consensus size: 208
360891 ATTTCGGGTC
* * * *
360901 GGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGGTTTTTTTAGGTGTGATATTCG
1 GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGG-TTTTTTAAGTGTGATATTCG
*
360966 GGTCGGGTCTGGTTCGGGTTTAGGGTGAAAAAAATCGGACCGACCCGAAAATATATATAATTCAG
65 GGTC--G---GGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAG
*
361031 GTCGGGTCGGATTAAGTCACAATTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGGT
125 GTCGGGTCGGATTAAGTCACAATTTTTATTAAATAAAAAT-ATTTTTTATTATTTCGGGTCAGGT
*
361096 TGGATTTCTAATTCATATATTT
189 CGGATTTCTAATTCATATA--T
*
361118 GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTCAAGTGTGATATTCGG
1 GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGG
*
361183 GTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCGGGTCGGG
66 GTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGG
** *
361248 TCGGATTAAGTCACTGTTTTTATTAAATAAAAATATTTTTTTTTATTTCGGGTCAGGTCGGATTT
131 TCGGATTAAGTCACAATTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCAGGTCGGATTT
361313 CTAATTCATATAT
196 CTAATTCATATAT
* * * * * *
361326 ---TCGGGTCGGATAAAATTTTATTTTGTTTGGGTCGGGTAGGGTTTTTTAAATTTGATATTCGG
1 GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGG
*
361388 GTCGAG-TCGGGT
66 GTCGGGTTCGGGT
361400 CAGGTTTTTT
Statistics
Matches: 262, Mismatches: 20, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
204 6 0.02
205 60 0.23
208 1 0.00
210 40 0.15
211 91 0.35
214 1 0.00
216 22 0.08
217 41 0.16
ACGTcount: A:0.23, C:0.12, G:0.28, T:0.37
Consensus pattern (208 bp):
GGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATATTCGG
GTCGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATTCAGGTCGGG
TCGGATTAAGTCACAATTTTTATTAAATAAAAATATTTTTTATTATTTCGGGTCAGGTCGGATTT
CTAATTCATATAT
Found at i:361398 original size:37 final size:37
Alignment explanation
Indices: 361355--361443 Score: 108
Period size: 38 Copynumber: 2.4 Consensus size: 37
361345 ATTTTGTTTG
*
361355 GGTCGGGTAGGGTTTTTTAAATTTGATATTCGGGTC-
1 GGTCGGGTAGGGTTTTTTAAATGTGATATTCGGGTCA
* * *
361391 GAGTCGGGTCAGGTTTTTTTAAGTGTGATATTCGGTTCA
1 G-GTCGGGT-AGGGTTTTTTAAATGTGATATTCGGGTCA
*
361430 GGTCGGGTTGGGTT
1 GGTCGGGTAGGGTT
361444 CTAGTTTAGG
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
36 1 0.02
37 11 0.25
38 31 0.70
39 1 0.02
ACGTcount: A:0.15, C:0.09, G:0.36, T:0.40
Consensus pattern (37 bp):
GGTCGGGTAGGGTTTTTTAAATGTGATATTCGGGTCA
Found at i:362944 original size:93 final size:91
Alignment explanation
Indices: 362827--363008 Score: 303
Period size: 93 Copynumber: 2.0 Consensus size: 91
362817 AATAATATTC
* * *
362827 GCCTCATTTATACCACTCAAATCTGCACCTTTATTAAGGATTGAAAGGCTA-AATGTGGATATCT
1 GCCTCATTTATACCACTCAAATCTGCACCTTCATTAAGGATTGAAAGG-TAGAAAGTGGACATCT
362891 CCTCACCTATTTCTGATATAAAGAAAAAG
65 CCTCACCTATTTCTGATA-AAA-AAAAAG
362920 GCCTCATTTATACCACTCAAATCTGCACCTTCATTAAGGATTGAAAGGTAGAAAGTGGACATCTC
1 GCCTCATTTATACCACTCAAATCTGCACCTTCATTAAGGATTGAAAGGTAGAAAGTGGACATCTC
362985 CTCACCTATTTCTGATAAAAAAAA
66 CTCACCTATTTCTGATAAAAAAAA
363009 GGGTGGGGTA
Statistics
Matches: 85, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
91 4 0.05
92 5 0.06
93 76 0.89
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (91 bp):
GCCTCATTTATACCACTCAAATCTGCACCTTCATTAAGGATTGAAAGGTAGAAAGTGGACATCTC
CTCACCTATTTCTGATAAAAAAAAAG
Found at i:365687 original size:29 final size:28
Alignment explanation
Indices: 365650--365789 Score: 104
Period size: 29 Copynumber: 4.9 Consensus size: 28
365640 AACAAGACAT
*
365650 GGATGTAATCCCTTGCAGAATCAGGACG
1 GGATATAATCCCTTGCAGAATCAGGACG
* * *
365678 GTGATATAATCTCATGCAGAATCAGGATAG
1 G-GATATAATCCCTTGCAGAATCAGGA-CG
* *
365708 GGATATAATCTCATT-TAGAATCAGGACG
1 GGATATAATC-CCTTGCAGAATCAGGACG
* * *
365736 GGAATATAGT-CTTGTGCAAAATCAGGACGG
1 GG-ATATAATCCCT-TGCAGAATCAGGAC-G
* * *
365766 GGATATATTCCCATGCAAAATCAG
1 GGATATAATCCCTTGCAGAATCAG
365790 AAATGCATCA
Statistics
Matches: 88, Mismatches: 16, Indels: 15
0.74 0.13 0.13
Matches are distributed among these distances:
27 2 0.02
28 5 0.06
29 74 0.84
30 7 0.08
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25
Consensus pattern (28 bp):
GGATATAATCCCTTGCAGAATCAGGACG
Found at i:365788 original size:58 final size:58
Alignment explanation
Indices: 365645--365789 Score: 148
Period size: 58 Copynumber: 2.5 Consensus size: 58
365635 ATAAAAACAA
* * * *
365645 GACATGGATGTAATCCCTTGCAGAATCAGGACGGTGATATAATCTCATGCAGAATCAG
1 GACAGGGATATAATCCCATGCAGAATCAGGACGGTGATATAATCTCATGCAAAATCAG
* * ** * **
365703 GATAGGGATATAATCTCATTTAGAATCAGGACGG-GAATATAGTCTTGTGCAAAATCAG
1 GACAGGGATATAATCCCATGCAGAATCAGGACGGTG-ATATAATCTCATGCAAAATCAG
* * *
365761 GACGGGGATATATTCCCATGCAAAATCAG
1 GACAGGGATATAATCCCATGCAGAATCAG
365790 AAATGCATCA
Statistics
Matches: 68, Mismatches: 18, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
57 1 0.01
58 67 0.99
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.25
Consensus pattern (58 bp):
GACAGGGATATAATCCCATGCAGAATCAGGACGGTGATATAATCTCATGCAAAATCAG
Found at i:365857 original size:2 final size:2
Alignment explanation
Indices: 365850--365879 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
365840 AACATATCAA
*
365850 AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
365880 TACGAACATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:374259 original size:18 final size:18
Alignment explanation
Indices: 374233--374277 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
374223 TACGACGTTC
* *
374233 CCACGTCTAAACTTAACA
1 CCACTTCTAAACTCAACA
374251 CCACTTCTAAACTCAACA
1 CCACTTCTAAACTCAACA
374269 CCACTTCTA
1 CCACTTCTA
374278 GTTTAGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.36, C:0.38, G:0.02, T:0.24
Consensus pattern (18 bp):
CCACTTCTAAACTCAACA
Found at i:379435 original size:29 final size:27
Alignment explanation
Indices: 379403--379496 Score: 100
Period size: 29 Copynumber: 3.3 Consensus size: 27
379393 TTTCATATGC
379403 AGAATCAAGACATGGATATAATCCCAT-A
1 AGAATC-AGACA-GGATATAATCCCATGA
* *
379431 TAGAATCAGTACGGGATATAAACCCATGA
1 -AGAATCAG-ACAGGATATAATCCCATGA
379460 AGAATCAGAGCAGAGATATAATCCCATGA
1 AGAATCAGA-CAG-GATATAATCCCATGA
*
379489 AAAATCAG
1 AGAATCAG
379497 GATGGGGATA
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
27 1 0.02
28 25 0.45
29 30 0.54
ACGTcount: A:0.46, C:0.17, G:0.18, T:0.19
Consensus pattern (27 bp):
AGAATCAGACAGGATATAATCCCATGA
Found at i:379450 original size:28 final size:28
Alignment explanation
Indices: 379416--379515 Score: 98
Period size: 29 Copynumber: 3.5 Consensus size: 28
379406 ATCAAGACAT
379416 GGATATAATCCCAT-ATAGAATCAGTA-CG
1 GGATATAATCCCATGA-AGAATCAG-AGCG
*
379444 GGATATAAACCCATGAAGAATCAGAGCAG
1 GGATATAATCCCATGAAGAATCAGAGC-G
* *
379473 AGATATAATCCCATGAAAAATCAGGATG-G
1 GGATATAATCCCATGAAGAATCA-GA-GCG
*
379502 GGATATATTCCCAT
1 GGATATAATCCCAT
379516 ACAGAACAAG
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
27 1 0.02
28 22 0.36
29 35 0.57
30 2 0.03
31 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (28 bp):
GGATATAATCCCATGAAGAATCAGAGCG
Found at i:379619 original size:18 final size:18
Alignment explanation
Indices: 379596--379643 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
379586 ATATCTATAA
*
379596 ATGTGTGTGTGTG-CATGT
1 ATGTGTGTGTGTGTC-TAT
*
379614 ATGTGTTTGTGTGTCTAT
1 ATGTGTGTGTGTGTCTAT
379632 ATGTGTGTGTGT
1 ATGTGTGTGTGT
379644 ATATATTCAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 25 0.96
19 1 0.04
ACGTcount: A:0.10, C:0.04, G:0.35, T:0.50
Consensus pattern (18 bp):
ATGTGTGTGTGTGTCTAT
Found at i:379640 original size:16 final size:16
Alignment explanation
Indices: 379596--379649 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 16
379586 ATATCTATAA
*
379596 ATGTGTGTGTGTGCATGT
1 ATGTGTGTGTGT-C-TAT
379614 ATGTGTTTGTGTGTCTAT
1 ATGTG--TGTGTGTCTAT
*
379632 ATGTGTGTGTGTATAT
1 ATGTGTGTGTGTCTAT
379648 AT
1 AT
379650 TCAGTTTATG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 12 0.38
18 12 0.38
19 1 0.03
20 7 0.22
ACGTcount: A:0.15, C:0.04, G:0.31, T:0.50
Consensus pattern (16 bp):
ATGTGTGTGTGTCTAT
Found at i:381092 original size:59 final size:59
Alignment explanation
Indices: 380913--381093 Score: 245
Period size: 59 Copynumber: 3.1 Consensus size: 59
380903 CTAACCCGAG
* * * * * *
380913 TATGACACATAAGGTCGTGCCCACAATCTACACTAGTTATACATTAGTGCAGTTCTGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCTGAA
* * * *
380972 TATGACACATAAGGTCGTGCCCACCATACGGACTAGTTATACTTTAGTGTAATCCCGAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCTGAA
* * *
381031 TATGACACATAAGGTCATGCCTACCATATGCACTAGTTATACTTTAGTGCAATCCTAAA
1 TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCTGAA
381090 TATG
1 TATG
381094 CAGCATACTG
Statistics
Matches: 105, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 105 1.00
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.29
Consensus pattern (59 bp):
TATGACACATAAGGTCGTGCCCACCATATGCACTAGTTATACTTTAGTGCAATCCTGAA
Found at i:384037 original size:23 final size:22
Alignment explanation
Indices: 384005--384084 Score: 81
Period size: 23 Copynumber: 3.5 Consensus size: 22
383995 TTTAAAAACA
*
384005 TATATAATATACGGTTTTAAAAT
1 TATAAAATATA-GGTTTTAAAAT
* *
384028 TATAACATATAGGTTTTAATAT
1 TATAAAATATAGGTTTTAAAAT
* *
384050 ATATATATATATA-GTTTTGAAAT
1 -TATA-AAATATAGGTTTTAAAAT
384073 TATAAAATATAG
1 TATAAAATATAG
384085 TTCTAAACAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 6 0.13
22 14 0.30
23 21 0.45
24 6 0.13
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.44
Consensus pattern (22 bp):
TATAAAATATAGGTTTTAAAAT
Found at i:384073 original size:45 final size:43
Alignment explanation
Indices: 384004--384308 Score: 146
Period size: 45 Copynumber: 6.9 Consensus size: 43
383994 TTTTAAAAAC
** * *
384004 ATATATA-ATATACGGTTTTAAAATTATAACATATAGGTTTTAA
1 ATATATATATATATAGTTTTGAAATTATAATATATA-GTTTTAA
* *
384047 TATATATATATATATAGTTTTGAAATTATAAAATATAGTTCTAAA
1 -ATATATATATATATAGTTTTGAAATTATAATATATAGTT-TTAA
* * *
384092 CATGTACATATATATAGTTTTGGAACTT-TAATATATAGTTTTCAA
1 -ATATATATATATATAGTTTT-GAAATTATAATATATAGTTTT-AA
* *
384137 A-ACATATA-ATATA-TTCTTGAAATTATGATATATAGTTCTTTTTAAA
1 ATATATATATATATAGTT-TTGAAATTATAATATATAG----TTTT-AA
* * * * *
384183 ATAAAAAAACATATATGTAATTTTCAAATTATAATATATAGTTTTGAA
1 AT----ATATATATATATAGTTTTGAAATTATAATATATAGTTTT-AA
* * *
384231 A-ACATATATATATA--TAT-ATA-TAT-ATATATAGTTTTTTAAA
1 ATATATATATATATAGTTTTGAAATTATAATATATAG--TTTT-AA
* * *
384271 ATATATATAATATATAATTTTAAAATTATAATTTATAG
1 ATATATAT-ATATATAGTTTTGAAATTATAATATATAG
384309 CCTTTTTGAA
Statistics
Matches: 202, Mismatches: 33, Indels: 49
0.71 0.12 0.17
Matches are distributed among these distances:
38 8 0.04
39 3 0.01
40 9 0.04
41 14 0.07
42 23 0.11
43 14 0.07
44 14 0.07
45 60 0.30
46 15 0.07
47 7 0.03
48 7 0.03
51 5 0.02
52 21 0.10
53 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (43 bp):
ATATATATATATATAGTTTTGAAATTATAATATATAGTTTTAA
Found at i:384084 original size:21 final size:21
Alignment explanation
Indices: 384007--384173 Score: 99
Period size: 21 Copynumber: 7.7 Consensus size: 21
383997 TAAAAACATA
** *
384007 TATAATATACGGTTTTAAAAT
1 TATAATATATAGTTTTGAAAT
*
384028 TATAACATATAGGTTTT-AATAT
1 TATAATATATA-GTTTTGAA-AT
384050 ATATATATATATAGTTTTGAAAT
1 -TATA-ATATATAGTTTTGAAAT
* * *
384073 TATAAAATATAGTTCTAAACAT
1 TATAATATATAGTTTTGAA-AT
* *
384095 GTACATATATATAGTTTTGGAACT
1 -TATA-ATATATAGTTTT-GAAAT
* *
384119 T-TAATATATAGTTTTCAAAACA
1 TATAATATATAGTTTT-GAAA-T
*
384141 TATAATATAT--TCTTGAAAT
1 TATAATATATAGTTTTGAAAT
*
384160 TATGATATATAGTT
1 TATAATATATAGTT
384174 CTTTTTAAAA
Statistics
Matches: 111, Mismatches: 22, Indels: 26
0.70 0.14 0.16
Matches are distributed among these distances:
19 9 0.08
20 3 0.03
21 40 0.36
22 15 0.14
23 23 0.21
24 19 0.17
25 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (21 bp):
TATAATATATAGTTTTGAAAT
Found at i:384241 original size:20 final size:20
Alignment explanation
Indices: 384188--384242 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
384178 TTAAAATAAA
*
384188 AAAACATATATGTAATTTTC
1 AAAACATATATATAATTTTC
** * *
384208 AAATTATAATATATAGTTTTG
1 AAAACAT-ATATATAATTTTC
384229 AAAACATATATATA
1 AAAACATATATATA
384243 TATATATATA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.40
Consensus pattern (20 bp):
AAAACATATATATAATTTTC
Found at i:384264 original size:38 final size:35
Alignment explanation
Indices: 384212--384286 Score: 105
Period size: 38 Copynumber: 2.1 Consensus size: 35
384202 ATTTTCAAAT
384212 TATAATATATAGTTTTGAAAACATATATATATATATA
1 TATAATATATAGTTTTGAAAA-ATATATATA-ATATA
**
384249 TATATATATATAGTTTTTTAAAATATATATAATATA
1 TATA-ATATATAGTTTTGAAAAATATATATAATATA
384285 TA
1 TA
384287 ATTTTAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
36 7 0.20
37 13 0.37
38 15 0.43
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (35 bp):
TATAATATATAGTTTTGAAAAATATATATAATATA
Found at i:384279 original size:2 final size:2
Alignment explanation
Indices: 384234--384260 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
384224 TTTTGAAAAC
384234 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
384261 GTTTTTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:384300 original size:25 final size:26
Alignment explanation
Indices: 384244--384300 Score: 75
Period size: 24 Copynumber: 2.3 Consensus size: 26
384234 ATATATATAT
*
384244 ATATATATATATATATAGTTTTTTAAA
1 ATATATATATATATATAG-ATTTTAAA
384271 ATATATATA-ATATATA-ATTTTAAA
1 ATATATATATATATATAGATTTTAAA
384295 AT-TATA
1 ATATATA
384301 ATTTATAGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 4 0.14
24 9 0.31
26 7 0.24
27 9 0.31
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (26 bp):
ATATATATATATATATAGATTTTAAA
Found at i:386376 original size:20 final size:20
Alignment explanation
Indices: 386321--386382 Score: 97
Period size: 20 Copynumber: 3.1 Consensus size: 20
386311 GGGCTTGATT
*
386321 CTACTGTAGCAGTATTGATA
1 CTACTGTAGCAGTATCGATA
*
386341 CTACTGCAGCAGTATCGATA
1 CTACTGTAGCAGTATCGATA
*
386361 CTACTGTAGCAGTATCAATA
1 CTACTGTAGCAGTATCGATA
386381 CT
1 CT
386383 CATTTTGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (20 bp):
CTACTGTAGCAGTATCGATA
Found at i:390435 original size:19 final size:19
Alignment explanation
Indices: 390411--390481 Score: 142
Period size: 19 Copynumber: 3.7 Consensus size: 19
390401 AATAGCCAGA
390411 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
390430 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
390449 GTGCATCGATGCATGGCTT
1 GTGCATCGATGCATGGCTT
390468 GTGCATCGATGCAT
1 GTGCATCGATGCAT
390482 CAAATGCACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 52 1.00
ACGTcount: A:0.17, C:0.21, G:0.31, T:0.31
Consensus pattern (19 bp):
GTGCATCGATGCATGGCTT
Found at i:390504 original size:45 final size:45
Alignment explanation
Indices: 390449--390534 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
390439 TGCATGGCTT
* *
390449 GTGCATCGATGCATGGCT-TGTGCATCGATGCATCAAATGCACTGA
1 GTGCATCGATGCATGG-TATGTGCATCAATGCATAAAATGCACTGA
390494 GTGCATCGATGCATGGTATGTGCATCAATGCATAAAATGCA
1 GTGCATCGATGCATGGTATGTGCATCAATGCATAAAATGCA
390535 TTCGATGTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
44 1 0.03
45 37 0.97
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (45 bp):
GTGCATCGATGCATGGTATGTGCATCAATGCATAAAATGCACTGA
Found at i:392933 original size:2 final size:2
Alignment explanation
Indices: 392926--392970 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
392916 CAAAAGAGTG
392926 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
392968 TA T
1 TA T
392971 TGCTTTGAAT
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:393979 original size:68 final size:67
Alignment explanation
Indices: 393920--394045 Score: 171
Period size: 68 Copynumber: 1.9 Consensus size: 67
393910 TAATATTTAT
* *
393920 GATAAAATGCTCAACAATAACAAAACCGGTAGCGCATAATAATGTTTCCGGTCATTTTTACCAAA
1 GATAAAATGCTCAACAATAACAAAACCGATAGCGCATAATAATG-TTCCGGTCATTTTTAACAAA
*
393985 TCC
65 TAC
* * * * *
393988 GGTAAAATGTTCAATAATAACAAAACCGATAGCGCCTAATAATGTTCTGGTCATTTTT
1 GATAAAATGCTCAACAATAACAAAACCGATAGCGCATAATAATGTTCCGGTCATTTTT
394046 TACTGGTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
67 13 0.25
68 39 0.75
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.29
Consensus pattern (67 bp):
GATAAAATGCTCAACAATAACAAAACCGATAGCGCATAATAATGTTCCGGTCATTTTTAACAAAT
AC
Found at i:394341 original size:17 final size:17
Alignment explanation
Indices: 394314--394356 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
394304 TTTCAATTCA
394314 TATTTAATTTAG-CATT
1 TATTTAATTTAGTCATT
394330 TATTTCAATTTAGTCA-T
1 TATTT-AATTTAGTCATT
394347 TAGTTTAATT
1 TA-TTTAATT
394357 CATGTAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 14 0.58
18 5 0.21
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (17 bp):
TATTTAATTTAGTCATT
Found at i:394599 original size:4 final size:4
Alignment explanation
Indices: 394590--394616 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
394580 TTTAGCTTTG
394590 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
394617 TAAATTTTTA
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:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:394960 original size:20 final size:20
Alignment explanation
Indices: 394923--394962 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
394913 TAGTTATAGG
*
394923 TTTAGTCCCTTAATTTTAGA
1 TTTAGTCCCTTAACTTTAGA
*
394943 TTTAGTCCCTTAGCTTTAGA
1 TTTAGTCCCTTAACTTTAGA
394963 CTTTTCACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.47
Consensus pattern (20 bp):
TTTAGTCCCTTAACTTTAGA
Found at i:395853 original size:89 final size:89
Alignment explanation
Indices: 395699--395882 Score: 341
Period size: 89 Copynumber: 2.1 Consensus size: 89
395689 CTTAAACCTG
* *
395699 ACGTTTTGATAAAATTAAAATATTTTATTAAAATTACCCAATTTTATGGTGTTCCAATCATACCT
1 ACGTTTTGATAAAAATAAAATATTTTATTAAAATTACCCAATTTTATGGTGTTCCAATCACACCT
395764 TAAAATGGTTGGTGGTGACTCCCA
66 TAAAATGGTTGGTGGTGACTCCCA
*
395788 ACGTTTTGATAAAAATAAAATATTTTATTAAAATTACCCGATTTTATGGTGTTCCAATCACACCT
1 ACGTTTTGATAAAAATAAAATATTTTATTAAAATTACCCAATTTTATGGTGTTCCAATCACACCT
395853 TAAAATGGTTGGTGGTGACTCCCA
66 TAAAATGGTTGGTGGTGACTCCCA
395877 ACGTTT
1 ACGTTT
395883 CCTAAAATCA
Statistics
Matches: 92, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
89 92 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (89 bp):
ACGTTTTGATAAAAATAAAATATTTTATTAAAATTACCCAATTTTATGGTGTTCCAATCACACCT
TAAAATGGTTGGTGGTGACTCCCA
Found at i:396133 original size:18 final size:20
Alignment explanation
Indices: 396090--396133 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
396080 ATGTTCCAGT
*
396090 AGTATCGATATTTACCCTTG
1 AGTATCGATATCTACCCTTG
396110 -GTATCGATA-CT-CCCTTG
1 AGTATCGATATCTACCCTTG
396127 AGTATCG
1 AGTATCG
396134 GTACCAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.27
18 7 0.32
19 9 0.41
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (20 bp):
AGTATCGATATCTACCCTTG
Found at i:396198 original size:20 final size:19
Alignment explanation
Indices: 396173--396222 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 19
396163 TTTGTTACTG
396173 GTATCGATACT-ACCCTCTGA
1 GTATCGATACTGACCC-C-GA
396193 GTATCGATACTGGACCCCGA
1 GTATCGATACT-GACCCCGA
396213 GTATCGATAC
1 GTATCGATAC
396223 CCTTTGAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 23 0.82
21 1 0.04
22 4 0.14
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (19 bp):
GTATCGATACTGACCCCGA
Found at i:399778 original size:3 final size:3
Alignment explanation
Indices: 399770--399806 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
399760 AGTCCCAAAA
399770 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
399807 TTGGAATTCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:408955 original size:16 final size:16
Alignment explanation
Indices: 408934--408964 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
408924 TCATATTTGA
408934 TTTATAAAAATATTAT
1 TTTATAAAAATATTAT
*
408950 TTTATAAAACTATTA
1 TTTATAAAAATATTA
408965 GGATATATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTATAAAAATATTAT
Found at i:412799 original size:7 final size:7
Alignment explanation
Indices: 412787--412811 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
412777 TTAAAAATTA
412787 TTTATAT
1 TTTATAT
412794 TTTATAT
1 TTTATAT
412801 TTTATAT
1 TTTATAT
412808 TTTA
1 TTTA
412812 AGTTTAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTATAT
Found at i:414359 original size:16 final size:16
Alignment explanation
Indices: 414338--414382 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
414328 TGATTTTTCT
*
414338 AAAATAATATAAATTA
1 AAAATAATATAAAATA
*
414354 AAAATAAAATAAAATA
1 AAAATAATATAAAATA
414370 AAAATAAATATAA
1 AAAAT-AATATAA
414383 TCGGATATCC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 19 0.76
17 6 0.24
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAATATAAAATA
Found at i:416491 original size:59 final size:59
Alignment explanation
Indices: 416393--416743 Score: 542
Period size: 59 Copynumber: 5.9 Consensus size: 59
416383 TAAATTCAAT
* * * *
416393 TGGAATTTCATACAAACAGTATGATTTCCTTATCC-TTTTAGCACACAGAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTA-CCATTTTAGCACACAAAGTGCCCTATC
* *
416452 TGGAAATTCATACACTTAGTATGATTTTCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
416511 TAGAAATTCATACACATAGTATGATTTTCTTACAATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* * *
416570 TGGAAATTCATACACATAGTATAATTTTCTTACCATTTTAGCACACAAAGTTCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
416629 TGGAAATTCATACACATAGTATGATTTCCTTACCAGTTTAGCACATAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
416688 TGGAAATTCATAGACATAATATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCT
416744 TTGGTAATTC
Statistics
Matches: 269, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
58 2 0.01
59 267 0.99
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (59 bp):
TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:417053 original size:19 final size:19
Alignment explanation
Indices: 417008--417054 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
416998 CAAAATATTT
*
417008 ATTATCAACTTCCTATAAC
1 ATTATCAGCTTCCTATAAC
417027 ATTATCAGCTTCCTATAAC
1 ATTATCAGCTTCCTATAAC
417046 ATTATCAGC
1 ATTATCAGC
417055 CCTAACTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (19 bp):
ATTATCAGCTTCCTATAAC
Found at i:417104 original size:21 final size:22
Alignment explanation
Indices: 417076--417133 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
417066 ATTTTCAACC
*
417076 CTTAGGTATCGATA-T-CCCTA
1 CTTAGGTATCGATACTACCCCA
*
417096 CTTATGGTATTGATACTACCCCA
1 CTTA-GGTATCGATACTACCCCA
417119 -TTAGGGTATCGATAC
1 CTTA-GGTATCGATAC
417134 CCCCTTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 4 0.13
21 9 0.29
22 14 0.45
23 4 0.13
ACGTcount: A:0.26, C:0.22, G:0.17, T:0.34
Consensus pattern (22 bp):
CTTAGGTATCGATACTACCCCA
Found at i:423710 original size:59 final size:59
Alignment explanation
Indices: 423343--423688 Score: 525
Period size: 59 Copynumber: 5.9 Consensus size: 59
423333 TAAATTCAAT
* * ** ** *
423343 TGGAATTTCATACAAACGGTATGATTTCCTTATCC-TTTTAGCACACAGTGTTCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTA-CCATTTTAGCACACAAAGTGCCCTATC
* *
423402 TGGAAATTCATACACTTAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATA
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
** *
423461 TGGAAATTCATACACATAGTATGATTTCCTTAATATTTTAGCACACAAAGTGCCCCATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
* *
423520 TGGAAACTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTGTC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
423579 TAGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
*
423638 TGGAAATTCATACACATAGTATGATTT-CTTACAATTTTAGCACACAAAGTG
1 TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTG
423689 ACCTTTGGTA
Statistics
Matches: 262, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
58 25 0.10
59 237 0.90
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.33
Consensus pattern (59 bp):
TGGAAATTCATACACATAGTATGATTTCCTTACCATTTTAGCACACAAAGTGCCCTATC
Found at i:424037 original size:21 final size:20
Alignment explanation
Indices: 424011--424082 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 20
424001 GCCCTTAGGT
424011 ATACCCCTGCTTATGGTATCG
1 ATACCCCT-CTTATGGTATCG
*
424032 ATACCCCTACTTATGGTATCA
1 ATACCCCT-CTTATGGTATCG
*
424053 ATACTACCC-CATTAGGGTATCG
1 ATAC--CCCTC-TTATGGTATCG
424075 ATACCCCT
1 ATACCCCT
424083 TCATGTATCA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
20 3 0.07
21 24 0.56
22 13 0.30
23 3 0.07
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.31
Consensus pattern (20 bp):
ATACCCCTCTTATGGTATCG
Found at i:424170 original size:22 final size:21
Alignment explanation
Indices: 424117--424173 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
424107 TTCGAAGTAA
*
424117 CATGGTATCGATA-CCCTCAT
1 CATGGTATCGATACCCCTAAT
424137 CATGGTATCGATACCCCTAAT
1 CATGGTATCGATACCCCTAAT
*
424158 CTATGGTACCGATACC
1 C-ATGGTATCGATACC
424174 TTCTAAGTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.39
21 7 0.21
22 13 0.39
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (21 bp):
CATGGTATCGATACCCCTAAT
Found at i:425207 original size:21 final size:22
Alignment explanation
Indices: 425176--425235 Score: 79
Period size: 21 Copynumber: 2.8 Consensus size: 22
425166 ATCTCAGTAG
425176 TGCTAAGGCACTTTAGTATTAA
1 TGCTAAGGCACTTTAGTATTAA
* *
425198 TGC-AATGCACTTTCA-TATTAG
1 TGCTAAGGCACTTT-AGTATTAA
425219 TGCTAAGGCACTTTAGT
1 TGCTAAGGCACTTTAGT
425236 TATTCAAGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 18 0.56
22 14 0.44
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.37
Consensus pattern (22 bp):
TGCTAAGGCACTTTAGTATTAA
Found at i:436237 original size:19 final size:18
Alignment explanation
Indices: 436193--436237 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
436183 AGATGATATC
436193 AAACATTAAACAACTTAA
1 AAACATTAAACAACTTAA
* * *
436211 TAATATTATAACAATTTAA
1 AAACATTA-AACAACTTAA
436230 AAACATTA
1 AAACATTA
436238 CATTTGAAGT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.31
Consensus pattern (18 bp):
AAACATTAAACAACTTAA
Found at i:446547 original size:31 final size:29
Alignment explanation
Indices: 446512--446573 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
446502 TTTAGTCTCA
*
446512 AAACTTTTCCAAACTTTATACTTTGGTCACT
1 AAACTTTT--AAAATTTATACTTTGGTCACT
**
446543 AAACTTTTAAAATTTATGTTTTGGTCACT
1 AAACTTTTAAAATTTATACTTTGGTCACT
446572 AA
1 AA
446574 CCAAAATTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 20 0.71
31 8 0.29
ACGTcount: A:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (29 bp):
AAACTTTTAAAATTTATACTTTGGTCACT
Found at i:449835 original size:23 final size:23
Alignment explanation
Indices: 449809--449882 Score: 139
Period size: 23 Copynumber: 3.2 Consensus size: 23
449799 ATATATATCC
*
449809 TTTTGTATTCAATCGTAACTCTA
1 TTTTGTATTCAGTCGTAACTCTA
449832 TTTTGTATTCAGTCGTAACTCTA
1 TTTTGTATTCAGTCGTAACTCTA
449855 TTTTGTATTCAGTCGTAACTCTA
1 TTTTGTATTCAGTCGTAACTCTA
449878 TTTTG
1 TTTTG
449883 ATTGAACTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.22, C:0.16, G:0.12, T:0.50
Consensus pattern (23 bp):
TTTTGTATTCAGTCGTAACTCTA
Found at i:453072 original size:23 final size:23
Alignment explanation
Indices: 453028--453072 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
453018 AATAATACAA
* *
453028 TTGACATTGGCATAATATTTTAG
1 TTGACATTGGAATAATAATTTAG
453051 TTGACATTGGGAAT-ATAATTTA
1 TTGACATT-GGAATAATAATTTA
453073 ATTTTTTGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.42
Consensus pattern (23 bp):
TTGACATTGGAATAATAATTTAG
Found at i:453878 original size:2 final size:2
Alignment explanation
Indices: 453867--453937 Score: 53
Period size: 2 Copynumber: 35.5 Consensus size: 2
453857 TGTAAACAAC
*
453867 TA TA -A TA TA TA TA TA TA TGA TGA -A TA CTA TGA TA CA TA TA T-
1 TA TA TA TA TA TA TA TA TA T-A T-A TA TA -TA T-A TA TA TA TA TA
453908 TA TA -A TA TA TA TA TA TA TA TA CT- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA T
453938 TGTAACGCCC
Statistics
Matches: 58, Mismatches: 2, Indels: 18
0.74 0.03 0.23
Matches are distributed among these distances:
1 5 0.09
2 44 0.76
3 9 0.16
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:457154 original size:18 final size:18
Alignment explanation
Indices: 457131--457170 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
457121 TTGTTTGATC
457131 GATAATTTGGTGCCATTA
1 GATAATTTGGTGCCATTA
*
457149 GATAATTTGGTGCCTTTA
1 GATAATTTGGTGCCATTA
457167 GATA
1 GATA
457171 CGTGAAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.40
Consensus pattern (18 bp):
GATAATTTGGTGCCATTA
Found at i:458463 original size:43 final size:43
Alignment explanation
Indices: 458331--458626 Score: 153
Period size: 43 Copynumber: 6.9 Consensus size: 43
458321 AGCGGCGTTG
* * *
458331 AGGTGTTGTTATTTAGCGGCG-TTTGTCACAAAAACGCCGCAAT
1 AGGTGTTGATATTTAGCGGCGTTTTTTCA-ACAAACGCCGCAAT
* * * *
458374 AAGT-TTGGATGTTTAGCGGCGTTTTACTT--ACAATCGCCGCAGT
1 AGGTGTT-GATATTTAGCGGCGTTTT--TTCAACAAACGCCGCAAT
* *
458417 AGGTGTTGATATTTTGCGGCGTTTTTTCAACAAACGACGCAAT
1 AGGTGTTGATATTTAGCGGCGTTTTTTCAACAAACGCCGCAAT
* * * * ** * *
458460 AGGTGATGTTGTTTAGCGGCG-TTTCTCCCCAAACGTCGCAGT
1 AGGTGTTGATATTTAGCGGCGTTTTTTCAACAAACGCCGCAAT
* * * * * * * *
458502 AGGTTTTCAGATTAAGCGGCGTTGTATCAA-AAATGACGCAAT
1 AGGTGTTGATATTTAGCGGCGTTTTTTCAACAAACGCCGCAAT
* * * * *
458544 AAGG-GTTGAGAATTAGCGGCGGTTTTATT-GA-AAACGTCGTAAT
1 -AGGTGTTGATATTTAGCGGC-GTTTT-TTCAACAAACGCCGCAAT
** *
458587 AGGTGTTGAGCTTTAGCGGC-ATTTTTCATACAAACGCCGC
1 AGGTGTTGATATTTAGCGGCGTTTTTTCA-ACAAACGCCGC
458627 TAAAGTTCGG
Statistics
Matches: 186, Mismatches: 52, Indels: 30
0.69 0.19 0.11
Matches are distributed among these distances:
40 2 0.01
41 5 0.03
42 57 0.31
43 115 0.62
44 6 0.03
46 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (43 bp):
AGGTGTTGATATTTAGCGGCGTTTTTTCAACAAACGCCGCAAT
Found at i:459043 original size:21 final size:19
Alignment explanation
Indices: 459018--459069 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
459008 ATTCTTCACA
459018 TCTCTGCTGATATACTGCTTC
1 TCTCTGCTG-T-TACTGCTTC
*
459039 TCTCTATGCTGTTGCTGCTTC
1 TCTC--TGCTGTTACTGCTTC
459060 TCTCTG-TGTT
1 TCTCTGCTGTT
459070 GCCGCTGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 4 0.14
19 2 0.07
21 16 0.57
22 1 0.04
23 5 0.18
ACGTcount: A:0.08, C:0.27, G:0.17, T:0.48
Consensus pattern (19 bp):
TCTCTGCTGTTACTGCTTC
Found at i:459076 original size:21 final size:21
Alignment explanation
Indices: 459032--459081 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
459022 TGCTGATATA
**
459032 CTGCTTCTCTCTATGCTGTTG
1 CTGCTTCTCTCTATGCTGCCG
* *
459053 CTGCTTCTCTCTGTGTTGCCG
1 CTGCTTCTCTCTATGCTGCCG
459074 CTGCTTCT
1 CTGCTTCT
459082 TTCTCCACTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.02, C:0.32, G:0.20, T:0.46
Consensus pattern (21 bp):
CTGCTTCTCTCTATGCTGCCG
Found at i:459131 original size:21 final size:21
Alignment explanation
Indices: 459051--459156 Score: 95
Period size: 21 Copynumber: 4.9 Consensus size: 21
459041 TCTATGCTGT
*
459051 TGCTGCTTCTCTCTGTGTTGCCGC
1 TGCTGC-TCTCTCTG-CTT-CCGC
* * **
459075 TGCTTCTTTCTCCACTTCCGC
1 TGCTGCTCTCTCTGCTTCCGC
* **
459096 TGCTGCTTTGGCTGCTTCCGC
1 TGCTGCTCTCTCTGCTTCCGC
*
459117 TGCTGCTCTCTCTGCTTCCAC
1 TGCTGCTCTCTCTGCTTCCGC
*
459138 TGTTGCTCTCTCTGCTTCC
1 TGCTGCTCTCTCTGCTTCC
459157 CTTGCTTCAT
Statistics
Matches: 67, Mismatches: 15, Indels: 3
0.79 0.18 0.04
Matches are distributed among these distances:
21 55 0.82
22 2 0.03
23 5 0.07
24 5 0.07
ACGTcount: A:0.02, C:0.38, G:0.19, T:0.42
Consensus pattern (21 bp):
TGCTGCTCTCTCTGCTTCCGC
Found at i:466692 original size:21 final size:23
Alignment explanation
Indices: 466652--466698 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
466642 ACGAAACATC
*
466652 ATTCTTGTTCAGTAAAAAAAC-A
1 ATTCGTGTTCAGTAAAAAAACTA
466674 ATTCGTGTTCAGT-AAAAAACTA
1 ATTCGTGTTCAGTAAAAAAACTA
466696 ATT
1 ATT
466699 GCTCGTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 7 0.30
22 16 0.70
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (23 bp):
ATTCGTGTTCAGTAAAAAAACTA
Found at i:468712 original size:41 final size:41
Alignment explanation
Indices: 468638--468856 Score: 239
Period size: 41 Copynumber: 5.3 Consensus size: 41
468628 TTTATACAAA
* * * *
468638 AAAAACTCCACTTTTGATT-ACATTATTGTGGCGTTTGCTA-
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTG-TAC
* * *
468678 ATAAACGACACTATTGTTTAACACTATTGCGGCGTTTGT-C
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTAC
* * *
468718 TAAAAATGCCACTGTTGATTAACACTATTGCGGCGTTTGTAT
1 -AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTAC
*
468760 AAAAACGCCATTATTGATTAACACTATTGCGGCGTTTGTAC
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTAC
* ** *
468801 AAAAATGCCACTATTGATTAACACTATTATGGCGTTT-TAGG
1 AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTA-C
468842 AACAAACGCCACTAT
1 AA-AAACGCCACTAT
468857 ATGCGTAATA
Statistics
Matches: 150, Mismatches: 23, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
40 17 0.11
41 122 0.81
42 11 0.07
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (41 bp):
AAAAACGCCACTATTGATTAACACTATTGCGGCGTTTGTAC
Found at i:468716 original size:22 final size:22
Alignment explanation
Indices: 468691--468757 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
468681 AACGACACTA
468691 TTGTTTAACACTATTGCGGCGT
1 TTGTTTAACACTATTGCGGCGT
* * **
468713 TTGTCTAA-A--AATGCCAC-T
1 TTGTTTAACACTATTGCGGCGT
*
468731 GTTGATTAACACTATTGCGGCGT
1 -TTGTTTAACACTATTGCGGCGT
468754 TTGT
1 TTGT
468758 ATAAAAACGC
Statistics
Matches: 30, Mismatches: 10, Indels: 10
0.60 0.20 0.20
Matches are distributed among these distances:
18 1 0.03
19 11 0.37
20 1 0.03
21 1 0.03
22 15 0.50
23 1 0.03
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.39
Consensus pattern (22 bp):
TTGTTTAACACTATTGCGGCGT
Found at i:468756 original size:82 final size:82
Alignment explanation
Indices: 468645--468837 Score: 266
Period size: 82 Copynumber: 2.4 Consensus size: 82
468635 AAAAAAAACT
* * * *
468645 CCACTTTTGATT-ACATTATTGTGGCGTTTGCTA-ATAAACGACACTATTGTTTAACACTATTGC
1 CCACTATTGATTAACACTATTGTGGCGTTTG-TATAAAAACGACACTATTGATTAACACTATTGC
468708 GGCGTTTGT-CTAAAAATG
65 GGCGTTTGTAC-AAAAATG
* * * *
468726 CCACTGTTGATTAACACTATTGCGGCGTTTGTATAAAAACGCCATTATTGATTAACACTATTGCG
1 CCACTATTGATTAACACTATTGTGGCGTTTGTATAAAAACGACACTATTGATTAACACTATTGCG
468791 GCGTTTGTACAAAAATG
66 GCGTTTGTACAAAAATG
*
468808 CCACTATTGATTAACACTATTATGGCGTTT
1 CCACTATTGATTAACACTATTGTGGCGTTT
468838 TAGGAACAAA
Statistics
Matches: 99, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
81 13 0.13
82 85 0.86
83 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.36
Consensus pattern (82 bp):
CCACTATTGATTAACACTATTGTGGCGTTTGTATAAAAACGACACTATTGATTAACACTATTGCG
GCGTTTGTACAAAAATG
Found at i:468984 original size:41 final size:41
Alignment explanation
Indices: 468907--468986 Score: 101
Period size: 41 Copynumber: 2.0 Consensus size: 41
468897 AGTTTACCAC
* *
468907 TCTATTGCGACGTTTTGGCTAAATCGCCGCAAAATTTATAA
1 TCTATTGCGACGTTTTGGATAAAACGCCGCAAAATTTATAA
*
468948 TCTATTGCGACGTTTAT-GATATAAACGCCGC-TAATTTAT
1 TCTATTGCGACGTTT-TGGATA-AAACGCCGCAAAATTTAT
468987 CACCCTATTG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 25 0.74
42 9 0.26
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (41 bp):
TCTATTGCGACGTTTTGGATAAAACGCCGCAAAATTTATAA
Found at i:470909 original size:18 final size:18
Alignment explanation
Indices: 470886--470921 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
470876 AAACATTCAA
470886 ACCTAGCCCCAAAACCAT
1 ACCTAGCCCCAAAACCAT
470904 ACCTAGCCCCAAAACCAT
1 ACCTAGCCCCAAAACCAT
470922 CTAGGTTCAT
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:0.39, C:0.44, G:0.06, T:0.11
Consensus pattern (18 bp):
ACCTAGCCCCAAAACCAT
Found at i:470953 original size:3 final size:3
Alignment explanation
Indices: 470945--470981 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
470935 GTGAAAGCAA
470945 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
470982 GTAGTAGCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:476785 original size:32 final size:31
Alignment explanation
Indices: 476739--476828 Score: 92
Period size: 32 Copynumber: 2.8 Consensus size: 31
476729 ACCAGATACT
*
476739 AGTCAGGTTTGCATTCAGATAATGCACAGCAG
1 AGTCAGG-TTGCATTCAGATAATGCACAACAG
* **
476771 AGTCAGGTTGGCATT-ATGATAATGCGCAATGG
1 AGTCAGGTT-GCATTCA-GATAATGCACAACAG
*
476803 AGTCAATGTTGCATTCAGATAATGCA
1 AGTC-AGGTTGCATTCAGATAATGCA
476829 TAAGAGTGTT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
31 3 0.06
32 40 0.83
33 5 0.10
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.28
Consensus pattern (31 bp):
AGTCAGGTTGCATTCAGATAATGCACAACAG
Found at i:478833 original size:14 final size:14
Alignment explanation
Indices: 478785--478833 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
478775 GGCCTCGAAA
* *
478785 ATATTTATTACAAT
1 ATATATATTATAAT
*
478799 ATTTATATTAT-AT
1 ATATATATTATAAT
478812 AGTATATATTATAAT
1 A-TATATATTATAAT
478827 ATATATA
1 ATATATA
478834 GTTTTCGAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 3 0.10
14 23 0.79
15 3 0.10
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (14 bp):
ATATATATTATAAT
Found at i:478897 original size:21 final size:22
Alignment explanation
Indices: 478841--478928 Score: 88
Period size: 22 Copynumber: 3.9 Consensus size: 22
478831 ATAGTTTTCG
*
478841 AATATAATTTTTGAAAATATAT
1 AATATAGTTTTTGAAAATATAT
*
478863 AATATAGTTTTTGAAAATGTAT
1 AATATAGTTTTTGAAAATATAT
* *
478885 TATTTAG-TTTTGAGAACATATAAT
1 AATATAGTTTTTGA-AA-ATAT-AT
*
478909 ATATATAGTTTTTTAAAATA
1 A-ATATAGTTTTTGAAAATA
478929 GTTTTTTTAG
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
21 6 0.11
22 27 0.51
23 3 0.06
24 5 0.09
25 7 0.13
26 5 0.09
ACGTcount: A:0.43, C:0.01, G:0.09, T:0.47
Consensus pattern (22 bp):
AATATAGTTTTTGAAAATATAT
Found at i:479000 original size:22 final size:22
Alignment explanation
Indices: 478960--479001 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
478950 ATATATATAA
*
478960 TTTTTGAAAACATATTATATGG
1 TTTTTGAAAACATAATATATGG
**
478982 TTTTTGAAAGTATAATATAT
1 TTTTTGAAAACATAATATAT
479002 ATTATATTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (22 bp):
TTTTTGAAAACATAATATATGG
Found at i:479035 original size:21 final size:22
Alignment explanation
Indices: 478992--479035 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
478982 TTTTTGAAAG
*
478992 TATAATATATATTATATTGTTT
1 TATAATATATATTATATTCTTT
*
479014 TATAATAT-TATTATTTTCTTT
1 TATAATATATATTATATTCTTT
479035 T
1 T
479036 TCTTTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (22 bp):
TATAATATATATTATATTCTTT
Found at i:479078 original size:34 final size:33
Alignment explanation
Indices: 479024--479103 Score: 87
Period size: 34 Copynumber: 2.5 Consensus size: 33
479014 TATAATATTA
* *
479024 TTATTTTC--TTTT-TCTTTTTTTCTTT-GTAT
1 TTATTTTCATTTTTATCTTTTTTTATTTACTAT
*
479053 TTACTTTTCATTTTTATCTTATTTTTATTTACTTT
1 TTA-TTTTCATTTTTATCTT-TTTTTATTTACTAT
479088 TTATTTTCATTTTTAT
1 TTATTTTCATTTTTAT
479104 TTTAGGTCCA
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
29 3 0.07
30 5 0.12
32 4 0.10
33 4 0.10
34 21 0.50
35 5 0.12
ACGTcount: A:0.14, C:0.10, G:0.01, T:0.75
Consensus pattern (33 bp):
TTATTTTCATTTTTATCTTTTTTTATTTACTAT
Found at i:479089 original size:12 final size:11
Alignment explanation
Indices: 479063--479105 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
479053 TTACTTTTCA
479063 TTTTTATCTTA-
1 TTTTTAT-TTAC
479074 TTTTTATTTAC
1 TTTTTATTTAC
*
479085 TTTTTATTTTC
1 TTTTTATTTAC
479096 ATTTTTATTT
1 -TTTTTATTT
479106 TAGGTCCAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 3 0.10
11 17 0.59
12 9 0.31
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTATTTAC
Found at i:479106 original size:28 final size:28
Alignment explanation
Indices: 479040--479107 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
479030 TCTTTTTCTT
* *
479040 TTTTTCTTTGTATTTACTTTTCATTTTTA
1 TTTTTATTT-TATTTACTTTTCATTTTCA
* *
479069 -TCTTATTTTTATTTACTTTTTATTTTCA
1 TTTTTA-TTTTATTTACTTTTCATTTTCA
479097 TTTTTATTTTA
1 TTTTTATTTTA
479108 GGTCCAATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
28 25 0.78
29 7 0.22
ACGTcount: A:0.16, C:0.09, G:0.01, T:0.74
Consensus pattern (28 bp):
TTTTTATTTTATTTACTTTTCATTTTCA
Found at i:484909 original size:18 final size:18
Alignment explanation
Indices: 484871--484909 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
484861 GAAATAACTG
* **
484871 AGGAAAAATTTATTTTCT
1 AGGAAAAATTAATTTGAT
484889 AGGAAAAATTAATTTGAT
1 AGGAAAAATTAATTTGAT
484907 AGG
1 AGG
484910 GCCAATGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.03, G:0.18, T:0.36
Consensus pattern (18 bp):
AGGAAAAATTAATTTGAT
Found at i:492352 original size:21 final size:22
Alignment explanation
Indices: 492328--492502 Score: 85
Period size: 22 Copynumber: 7.4 Consensus size: 22
492318 ATATATGATA
*
492328 ATATATATAGTTTTCAAAAATATAT
1 ATATATATAGTTTT--GAAATA-AT
492353 ATAATATATAGTTTTTG-AA-AAT
1 AT-ATATATAG-TTTTGAAATAAT
*
492375 ATATAATATAGTTTTTGAAA-CAT
1 ATAT-ATATAG-TTTTGAAATAAT
492398 AT-TATATAGTTTTGAAATCATAT
1 ATATATATAGTTTTGAAAT-A-AT
492421 AATATATATAGGTTTTGAAAATGTATAT
1 -ATATATATA-GTTTTG-AAA--TA-AT
*
492449 AATATATATAATTTTTGAAA-ACAT
1 -ATATATATAGTTTT-GAAATA-AT
* *
492473 AT-TATATAGTTTTTAAA-AGT
1 ATATATATAGTTTTGAAATAAT
492493 ATAATATATA
1 AT-ATATATA
492503 TTATAATGTT
Statistics
Matches: 126, Mismatches: 8, Indels: 35
0.75 0.05 0.21
Matches are distributed among these distances:
20 11 0.09
21 12 0.10
22 33 0.26
23 11 0.09
24 7 0.06
25 8 0.06
26 14 0.11
27 14 0.11
28 15 0.12
29 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (22 bp):
ATATATATAGTTTTGAAATAAT
Found at i:492474 original size:26 final size:26
Alignment explanation
Indices: 492325--492480 Score: 106
Period size: 26 Copynumber: 6.3 Consensus size: 26
492315 AGTATATATG
*
492325 ATAATATATAT-AGTTTTCAAAA-AT
1 ATAATATATATAAGTTTTGAAAACAT
492349 AT-ATATAATATATAGTTTTTG-AAA-AT
1 ATAATAT-ATATA-AG-TTTTGAAAACAT
492375 AT-ATA-ATAT-AGTTTTTG-AAAC--
1 ATAATATATATAAG-TTTTGAAAACAT
*
492396 AT-AT-TATAT-AGTTTTGAAATCAT
1 ATAATATATATAAGTTTTGAAAACAT
* *
492419 ATAATATATATAGGTTTTGAAAATGTAT
1 ATAATATATATAAGTTTTGAAAA--CAT
*
492447 ATAATATATATAATTTTTGAAAACAT
1 ATAATATATATAAGTTTTGAAAACAT
*
492473 ATTATATA
1 ATAATATA
492481 GTTTTTAAAA
Statistics
Matches: 109, Mismatches: 9, Indels: 26
0.76 0.06 0.18
Matches are distributed among these distances:
20 5 0.05
21 13 0.12
22 11 0.10
23 6 0.06
24 12 0.11
25 5 0.05
26 30 0.28
27 4 0.04
28 23 0.21
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (26 bp):
ATAATATATATAAGTTTTGAAAACAT
Found at i:492502 original size:22 final size:21
Alignment explanation
Indices: 492351--492428 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
492341 TCAAAAATAT
492351 ATATAATATATAGTTTTTGAAA
1 ATATAATATATAGTTTTT-AAA
*
492373 ATAT-ATAATATAGTTTTTGAA
1 ATATAAT-ATATAGTTTTTAAA
* * *
492394 ACATATTATATAGTTTTGAAA
1 ATATAATATATAGTTTTTAAA
492415 TCATATAATATATA
1 --ATATAATATATA
492429 TAGGTTTTGA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 19 0.42
22 16 0.36
23 10 0.22
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.45
Consensus pattern (21 bp):
ATATAATATATAGTTTTTAAA
Found at i:492519 original size:96 final size:94
Alignment explanation
Indices: 492325--492506 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 94
492315 AGTATATATG
* *
492325 ATAATATATATAGTTTTCAAAAATATATATAATATATAGTTTTTGAAAATATATAATATAGTTTT
1 ATAATATATATAGTTTTCAAAAATATATATAATATATAATTTTTGAAAACATATAATATAGTTTT
* * *
492390 TGAAACATATTATATAGTTTTGAAATCAT
66 TAAAACATAATATATAGTTATGAAATCAT
* * *
492419 ATAATATATATAGGTTTT-GAAAATGTATATAATATATATAATTTTTGAAAACATATTATATAGT
1 ATAATATATATA-GTTTTCAAAAATATATAT-A-ATATATAATTTTTGAAAACATATAATATAGT
*
492483 TTTTAAAAGTATAATATATA-TTAT
63 TTTTAAAA-CATAATATATAGTTAT
492507 AATGTTTTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
94 22 0.29
95 6 0.08
96 38 0.51
97 9 0.12
ACGTcount: A:0.45, C:0.02, G:0.08, T:0.45
Consensus pattern (94 bp):
ATAATATATATAGTTTTCAAAAATATATATAATATATAATTTTTGAAAACATATAATATAGTTTT
TAAAACATAATATATAGTTATGAAATCAT
Found at i:492538 original size:24 final size:22
Alignment explanation
Indices: 492511--492589 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 22
492501 TATTATAATG
492511 TTTTATAATTTTATTATTATTTTC
1 TTTTAT-ATTTTATT-TTATTTTC
* *
492535 TTTTTTATTTTTATTTTTATTTAC
1 TTTTATA-TTTTA-TTTTATTTTC
*
492559 TTTTCAT-TTTTATTTTATTTTA
1 TTTT-ATATTTTATTTTATTTTC
492581 TTTT-TATTT
1 TTTTATATTT
492590 ACTTTTTATT
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
20 1 0.02
21 3 0.07
22 12 0.26
23 6 0.13
24 21 0.46
25 3 0.07
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTATATTTTATTTTATTTTC
Found at i:492545 original size:6 final size:6
Alignment explanation
Indices: 492519--492607 Score: 84
Period size: 6 Copynumber: 15.5 Consensus size: 6
492509 TGTTTTATAA
* *
492519 TTTTAT TATTAT TTTCT-T TTTTAT TTTTAT TTTTA- -TTTACT TTTCAT
1 TTTTAT TTTTAT TTT-TAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT
492566 TTTTA- TTTTA- TTTTAT TTTTA- -TTTACT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTT
492608 AGTTCCAATA
Statistics
Matches: 70, Mismatches: 4, Indels: 18
0.76 0.04 0.20
Matches are distributed among these distances:
4 8 0.11
5 11 0.16
6 43 0.61
7 8 0.11
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTAT
Found at i:492562 original size:23 final size:23
Alignment explanation
Indices: 492519--492589 Score: 83
Period size: 23 Copynumber: 3.1 Consensus size: 23
492509 TGTTTTATAA
* *
492519 TTTTATTATTATTTTCTTTTTTAT
1 TTTTATTTTTATTTAC-TTTTTAT
*
492543 TTTTATTTTTATTTACTTTTCAT
1 TTTTATTTTTATTTACTTTTTAT
492566 TTTTA-TTTTATTTTA-TTTTTAT
1 TTTTATTTTTA-TTTACTTTTTAT
492588 TT
1 TT
492590 ACTTTTTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.31
23 15 0.36
24 14 0.33
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (23 bp):
TTTTATTTTTATTTACTTTTTAT
Found at i:492567 original size:17 final size:16
Alignment explanation
Indices: 492538--492606 Score: 95
Period size: 17 Copynumber: 4.2 Consensus size: 16
492528 TATTTTCTTT
492538 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
*
492554 TTTACTTTTCATTTTTA
1 TTTA-TTTTTATTTTTA
492571 TTT-TATTTTATTTTTA
1 TTTAT-TTTTATTTTTA
492587 TTTACTTTTTATTTTTA
1 TTTA-TTTTTATTTTTA
492604 TTT
1 TTT
492607 TAGTTCCAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.02
16 17 0.36
17 28 0.60
18 1 0.02
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:492585 original size:33 final size:34
Alignment explanation
Indices: 492537--492608 Score: 128
Period size: 33 Copynumber: 2.1 Consensus size: 34
492527 TTATTTTCTT
492537 TTTTATTTTTATTTTTATTTACTTTTCATTTTTA
1 TTTTATTTTTATTTTTATTTACTTTTCATTTTTA
*
492571 TTTTA-TTTTATTTTTATTTACTTTTTATTTTTA
1 TTTTATTTTTATTTTTATTTACTTTTCATTTTTA
492604 TTTTA
1 TTTTA
492609 GTTCCAATAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 32 0.86
34 5 0.14
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (34 bp):
TTTTATTTTTATTTTTATTTACTTTTCATTTTTA
Found at i:492608 original size:11 final size:11
Alignment explanation
Indices: 492518--492607 Score: 78
Period size: 11 Copynumber: 7.9 Consensus size: 11
492508 ATGTTTTATA
*
492518 ATTTTATTATT
1 ATTTTATTTTT
*
492529 ATTTTCTTTTTT
1 ATTTT-ATTTTT
492541 ATTTTTATTTTT
1 A-TTTTATTTTT
*
492553 A-TTTACTTTTC
1 ATTTTA-TTTTT
492564 ATTTT-TATTTT
1 ATTTTAT-TTTT
492575 ATTTTATTTTT
1 ATTTTATTTTT
492586 A-TTTACTTTTT
1 ATTTTA-TTTTT
492597 ATTTTTATTTT
1 A-TTTTATTTT
492608 AGTTCCAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 17
0.75 0.06 0.20
Matches are distributed among these distances:
10 9 0.14
11 29 0.45
12 19 0.29
13 8 0.12
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:502347 original size:38 final size:38
Alignment explanation
Indices: 502287--502389 Score: 144
Period size: 38 Copynumber: 2.8 Consensus size: 38
502277 TTGAAGCCAT
502287 ATGGA-AA-ATAT-ATTTTACAGGTCGGGTCGGATCGA-
1 ATGGAGAATATATAATTTTACAGGTCGGGTCGGAT-GAG
*
502322 ATGGAGAATATATAATTTTACAGGTCGGGTCGGATTAG
1 ATGGAGAATATATAATTTTACAGGTCGGGTCGGATGAG
*
502360 ATGAAGAATATATAATTTT-CAGGTCGGGTC
1 ATGGAGAATATATAATTTTACAGGTCGGGTC
502390 AAATTTGGAT
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
35 5 0.08
36 2 0.03
37 16 0.26
38 39 0.63
ACGTcount: A:0.32, C:0.10, G:0.27, T:0.31
Consensus pattern (38 bp):
ATGGAGAATATATAATTTTACAGGTCGGGTCGGATGAG
Found at i:519036 original size:121 final size:122
Alignment explanation
Indices: 518822--519060 Score: 462
Period size: 121 Copynumber: 2.0 Consensus size: 122
518812 GTTAAGCTCT
*
518822 GCACCCATTCTCTGTCTTCTCAATTTTCTAACACTTTCGAGCTAGAATGTAATGCTTTAGGTATA
1 GCACCCATTCTCTATCTTCTCAATTTTCTAACACTTTCGAGCTAGAATGTAATGCTTTAGGTATA
518887 GGCATAGACGTAGTTCTTATGAAAGAAAGATAACTTATTGCTTAC-TTAGTGAGAAG
66 GGCATAGACGTAGTTCTTATGAAAGAAAGATAACTTATTGCTTACTTTAGTGAGAAG
518943 GCACCCATTCTCTATCTTCTCAATTTTCTAACACTTTCGAGCTAGAATGTAATGCTTTAGGTATA
1 GCACCCATTCTCTATCTTCTCAATTTTCTAACACTTTCGAGCTAGAATGTAATGCTTTAGGTATA
519008 GGCATAGACGTAGTTCTTATGAAAGAAAGATAACTTATTGCTTACTTTAGTGA
66 GGCATAGACGTAGTTCTTATGAAAGAAAGATAACTTATTGCTTACTTTAGTGA
519061 AGTTAAAAGC
Statistics
Matches: 116, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
121 109 0.94
122 7 0.06
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (122 bp):
GCACCCATTCTCTATCTTCTCAATTTTCTAACACTTTCGAGCTAGAATGTAATGCTTTAGGTATA
GGCATAGACGTAGTTCTTATGAAAGAAAGATAACTTATTGCTTACTTTAGTGAGAAG
Found at i:521634 original size:14 final size:15
Alignment explanation
Indices: 521615--521643 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
521605 TTCAAACATC
521615 CATATC-ATCCAAAA
1 CATATCAATCCAAAA
521629 CATATCAATCCAAAA
1 CATATCAATCCAAAA
521644 ACATCCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.21
Consensus pattern (15 bp):
CATATCAATCCAAAA
Found at i:522982 original size:20 final size:21
Alignment explanation
Indices: 522945--522984 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
522935 CAACATAATT
*
522945 AAATCAAAAACAATAATTTTA
1 AAATCAAAAACAACAATTTTA
522966 AAATCAAAAAC-ACAATTTT
1 AAATCAAAAACAACAATTTT
522985 TTTAATTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATCAAAAACAACAATTTTA
Found at i:525020 original size:25 final size:25
Alignment explanation
Indices: 524986--525036 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
524976 ATGGATCGCC
524986 TATAATTTTACCATCATTGACATAG
1 TATAATTTTACCATCATTGACATAG
525011 TATAATTTTACCATCATTGACATAG
1 TATAATTTTACCATCATTGACATAG
525036 T
1 T
525037 TGTATTCTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.08, T:0.41
Consensus pattern (25 bp):
TATAATTTTACCATCATTGACATAG
Found at i:534789 original size:17 final size:18
Alignment explanation
Indices: 534767--534800 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
534757 TCAACCGGTC
534767 CGGTTC-GAACGGTTCAG
1 CGGTTCTGAACGGTTCAG
*
534784 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
534801 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.15, C:0.26, G:0.32, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAG
Done.