Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1839
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: 70880
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:1177 original size:81 final size:79
Alignment explanation
Indices: 1042--1242 Score: 210
Period size: 81 Copynumber: 2.5 Consensus size: 79
1032 ATAACGAGGG
* * ** * *
1042 TTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTA
1 TTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTA
1105 GAAAAAAAAAAATCGGGA
64 G--AAAAAAAAATCGGGA
* *
1123 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
* * * *
1188 GAATAAAGTCGGGG
66 AAAAAAAATCGGGA
* *
1202 TTGGAGTATTCCC-TCGGAAGTAACGGGGTTGGAGTATCCCC
1 TTGGAGTA-TCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
1243 GATGAAATAA
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
79 44 0.43
80 11 0.11
81 48 0.47
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.26
Consensus pattern (79 bp):
TTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
AAAAAAAATCGGGA
Found at i:1228 original size:28 final size:28
Alignment explanation
Indices: 1197--1266 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
1187 GGAATAAAGT
*
1197 CGGGGTTGGAGTATTCCCTCG-GAAGTAA
1 CGGGGTTGGAGTATTCCC-CGAGAAATAA
1225 CGGGGTTGGAGTA-TCCCCGATGAAATAA
1 CGGGGTTGGAGTATTCCCCGA-GAAATAA
*
1253 CGAGGTTGGAGTAT
1 CGGGGTTGGAGTAT
1267 CCTCGATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
26 2 0.05
27 4 0.11
28 31 0.84
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATTCCCCGAGAAATAA
Found at i:1346 original size:52 final size:52
Alignment explanation
Indices: 1290--1426 Score: 170
Period size: 52 Copynumber: 2.6 Consensus size: 52
1280 AAATTGGTAT
*
1290 TTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGG-AAAATTAGCG
1 TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCGATT-AAGGAAAAATTAGCG
* ** *
1342 TTTTGAAAATAAAACCAGGA-TTGGAGTATCCCCGATTGTGGAAAAATTAGTG
1 TTTTGGAAATAAAACC-GGAGTTGGAGTATCCCCGATTAAGGAAAAATTAGCG
* * *
1394 TTTTAGCAATAAAACCGGGGTTGGAGTATCCCC
1 TTTTGGAAATAAAACCGGAGTTGGAGTATCCCC
1427 TCAGAAATAA
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
51 4 0.05
52 66 0.90
53 3 0.04
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (52 bp):
TTTTGGAAATAAAACCGGAGTTGGAGTATCCCCGATTAAGGAAAAATTAGCG
Found at i:1472 original size:27 final size:27
Alignment explanation
Indices: 1409--1511 Score: 154
Period size: 27 Copynumber: 3.8 Consensus size: 27
1399 GCAATAAAAC
* *
1409 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATG-ATTAA
1437 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGATGATTAA
*
1464 CGGGGTTGGAGTATCCCCAATGATTAA
1 CGGGGTTGGAGTATCCCCGATGATTAA
1491 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1512 TGTGAAGAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
27 51 0.73
28 19 0.27
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.24
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGATGATTAA
Found at i:4002 original size:13 final size:13
Alignment explanation
Indices: 3984--4009 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3974 ACAAAGATCC
3984 ATGTATCGATACA
1 ATGTATCGATACA
3997 ATGTATCGATACA
1 ATGTATCGATACA
4010 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4005 original size:33 final size:33
Alignment explanation
Indices: 3963--4029 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3953 AAAATTTCCA
***
3963 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
3996 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
4029 A
1 A
4030 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:4073 original size:19 final size:18
Alignment explanation
Indices: 4049--4116 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
4039 CAGTAGCTAA
4049 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
4068 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
4083 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
4100 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
4117 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:4089 original size:13 final size:13
Alignment explanation
Indices: 4071--4095 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4061 ACAATACTTA
4071 TGTATCGATACAT
1 TGTATCGATACAT
4084 TGTATCGATACA
1 TGTATCGATACA
4096 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4093 original size:32 final size:32
Alignment explanation
Indices: 4052--4114 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
4042 TAGCTAATTA
*
4052 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
4084 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
4115 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:6484 original size:15 final size:14
Alignment explanation
Indices: 6443--6493 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 14
6433 TAAAAGTATC
*
6443 ATTTTGATTTTTAT
1 ATTTTAATTTTTAT
*
6457 ATTATT-ATATTTAAT
1 ATT-TTAAT-TTTTAT
6472 ATTTTAATTTTTAT
1 ATTTTAATTTTTAT
6486 AATTTTAA
1 -ATTTTAA
6494 AATTATAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
ATTTTAATTTTTAT
Found at i:6577 original size:21 final size:23
Alignment explanation
Indices: 6553--6599 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
6543 AGAATCGATA
*
6553 AAATTTTA-ATAAAAAA-ATTTT
1 AAATTTTATATAAAAAATAATTT
6574 AAATTTTATATAAAAAATAATTT
1 AAATTTTATATAAAAAATAATTT
6597 AAA
1 AAA
6600 CCCAATCTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.35
22 8 0.35
23 7 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATTTTATATAAAAAATAATTT
Found at i:6712 original size:17 final size:18
Alignment explanation
Indices: 6679--6723 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 18
6669 AATAGTTAAA
6679 TAATT-TTTTAATATTAT
1 TAATTATTTTAATATTAT
*
6696 TAATTATTTTTAT-TTAT
1 TAATTATTTTAATATTAT
6713 TAA-TATTTTAA
1 TAATTATTTTAA
6724 AAATTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 7 0.28
17 12 0.48
18 6 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TAATTATTTTAATATTAT
Found at i:6738 original size:15 final size:15
Alignment explanation
Indices: 6720--6774 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
6710 TATTAATATT
*
6720 TTAAAAATTTTAAAA
1 TTAAAAATATTAAAA
*
6735 TT-AAAATATTAAAT
1 TTAAAAATATTAAAA
* *
6749 TTAATAATATAAAAA
1 TTAAAAATATTAAAA
6764 TTAAAATATAT
1 TTAAAA-ATAT
6775 ATTATTTTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
14 12 0.38
15 16 0.50
16 4 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
TTAAAAATATTAAAA
Found at i:6746 original size:14 final size:14
Alignment explanation
Indices: 6723--6772 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 14
6713 TAATATTTTA
*
6723 AAAATTTTAAAATT
1 AAAATATTAAAATT
*
6737 AAAATATTAAATTT
1 AAAATATTAAAATT
*
6751 AATAATATAAAAATT
1 AA-AATATTAAAATT
6766 AAAATAT
1 AAAATAT
6773 ATATTATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 19 0.61
15 12 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATATTAAAATT
Found at i:6750 original size:21 final size:21
Alignment explanation
Indices: 6728--6768 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
6718 TTTTAAAAAT
6728 TTTAA-AAT-TAAAATATTAAA
1 TTTAATAATATAAAA-ATTAAA
6748 TTTAATAATATAAAAATTAAA
1 TTTAATAATATAAAAATTAAA
6769 ATATATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.26
21 9 0.47
22 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
TTTAATAATATAAAAATTAAA
Found at i:7607 original size:11 final size:11
Alignment explanation
Indices: 7591--7619 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
7581 AGGAAATTGT
7591 TTTATTTATTA
1 TTTATTTATTA
7602 TTTATTTATTA
1 TTTATTTATTA
7613 TTTATTT
1 TTTATTT
7620 TTGTGTTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTATTA
Found at i:7693 original size:15 final size:15
Alignment explanation
Indices: 7675--7708 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
7665 ATTATTTTAT
*
7675 ATCACTTTATTTCTC
1 ATCACTCTATTTCTC
*
7690 ATCACTCTATTTTTC
1 ATCACTCTATTTCTC
7705 ATCA
1 ATCA
7709 ATTTTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (15 bp):
ATCACTCTATTTCTC
Found at i:8329 original size:13 final size:13
Alignment explanation
Indices: 8311--8336 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
8301 CAAGGAAATA
8311 TATCGATACATTG
1 TATCGATACATTG
8324 TATCGATACATTG
1 TATCGATACATTG
8337 ATCTTTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TATCGATACATTG
Found at i:8398 original size:20 final size:19
Alignment explanation
Indices: 8373--8442 Score: 95
Period size: 20 Copynumber: 3.5 Consensus size: 19
8363 TTTACTCAGA
8373 TGTATCGATACATTTTGCAT
1 TGTATCGATACATTTT-CAT
*
8393 TGTATCGATACATTGCTCAT
1 TGTATCGATACATT-TTCAT
*
8413 TGTATCGATACATTTTACAA
1 TGTATCGATACATTTT-CAT
8433 TGTATCGATA
1 TGTATCGATA
8443 TATTCAAGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 1 0.02
20 43 0.96
21 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (19 bp):
TGTATCGATACATTTTCAT
Found at i:10822 original size:51 final size:51
Alignment explanation
Indices: 10731--10910 Score: 177
Period size: 51 Copynumber: 3.5 Consensus size: 51
10721 TAAATTTCTA
* * * **
10731 AATTTTTCAC-CTTGGGGATACTCCAA-TCCCGGTTCCATTTCCAAAACATC
1 AATTTTTCACAATCGGGGATACTCCAACT-CCGATTTTATTTCCAAAACATC
** * *
10781 AATTTTTCTTAATCGGGGATACTCCAACTCCGATTTTATTTCTAAAGCATC
1 AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATC
* * * * *
10832 GATTTATCACAATCGGAGATACTCTAACTCCGATTTTATTTTCAAAACA-C
1 AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATC
* *
10882 TAATTTTTCACAATTGAGGATACTCCAAC
1 -AATTTTTCACAATCGGGGATACTCCAAC
10911 CCTGTTATTT
Statistics
Matches: 103, Mismatches: 24, Indels: 5
0.78 0.18 0.04
Matches are distributed among these distances:
50 9 0.09
51 93 0.90
52 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (51 bp):
AATTTTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACATC
Found at i:10931 original size:28 final size:27
Alignment explanation
Indices: 10899--10970 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 27
10889 TCACAATTGA
*
10899 GGATACTCCAACCCTGTTATTTCATCG-G
1 GGATACTCCAACCCCGTTATTT--TCGAG
10927 GGATACTCCAACCCCGTTATTTTCGAG
1 GGATACTCCAACCCCGTTATTTTCGAG
10954 GGAATACTCCAACCCCG
1 GG-ATACTCCAACCCCG
10971 GCTTTATATC
Statistics
Matches: 41, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
26 3 0.07
27 3 0.07
28 35 0.85
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (27 bp):
GGATACTCCAACCCCGTTATTTTCGAG
Found at i:11045 original size:28 final size:29
Alignment explanation
Indices: 11004--11079 Score: 104
Period size: 28 Copynumber: 2.7 Consensus size: 29
10994 TTTTTTCATA
*
11004 ATCGGGG-TACTCCAACCCCGTTATTT-C
1 ATCGGGGATACTCCAAACCCGTTATTTCC
*
11031 ATCGGGGATACTCCAATCCCGTTATTTCC
1 ATCGGGGATACTCCAAACCCGTTATTTCC
*
11060 A-AGGGGATACTCCAAACCCG
1 ATCGGGGATACTCCAAACCCG
11080 ATTTTATTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 7 0.16
28 35 0.80
29 2 0.05
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.25
Consensus pattern (29 bp):
ATCGGGGATACTCCAAACCCGTTATTTCC
Found at i:11177 original size:51 final size:50
Alignment explanation
Indices: 11062--11178 Score: 189
Period size: 51 Copynumber: 2.3 Consensus size: 50
11052 TTATTTCCAA
* *
11062 GGGGATACTCCAAACCCGATTTTATTTCTAAAATACCAATTTCCCACAATC
1 GGGGATACTCC-AACCCGATTTTATTTCCAAAACACCAATTTCCCACAATC
*
11113 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATC
1 GGGGATACTCCAAC-CCGATTTTATTTCCAAAACACCAATTTCCCACAATC
11164 GGGGATACTCCAACC
1 GGGGATACTCCAACC
11179 TCGTTATTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
50 4 0.06
51 58 0.94
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (50 bp):
GGGGATACTCCAACCCGATTTTATTTCCAAAACACCAATTTCCCACAATC
Found at i:11195 original size:79 final size:79
Alignment explanation
Indices: 11112--11332 Score: 227
Period size: 79 Copynumber: 2.8 Consensus size: 79
11102 TTCCCACAAT
*
11112 CGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCACAATCGGGGATACTCCAA
1 CGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCATAATCGGGGATACTCCAA
*
11177 -CCTCGTTATTTTCG
66 CCCT-ATTATTTTCG
* * * * ** *
11191 CGGGGATACTCCAAC-CCTGATTTTATTTTCAAAATACTATTTTCT-ATAATTAGGGATACTCTA
1 CGGGGATACTCCAACTCC-GATTTTATTTCCAAAACACCAATTTCTCATAATCGGGGATACTCCA
11254 ACCCTATTATTTTCG
65 ACCCTATTATTTTCG
* * * * *
11269 AGGGGATACTCCAA-TCCCAATTTTTATTTCTAGAAACACCGATTT-TCCATAATCGAGGATACT
1 CGGGGATACTCCAACT-CCGA-TTTTATTTCCA-AAACACCAATTTCT-CATAATCGGGGATACT
11332 C
62 C
11333 TAGCCCAGTT
Statistics
Matches: 114, Mismatches: 20, Indels: 14
0.77 0.14 0.09
Matches are distributed among these distances:
78 40 0.35
79 53 0.46
80 8 0.07
81 13 0.11
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (79 bp):
CGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCATAATCGGGGATACTCCAA
CCCTATTATTTTCG
Found at i:14250 original size:13 final size:13
Alignment explanation
Indices: 14232--14279 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
14222 AAAATTTTAT
14232 TTTCTTTTAAGAA
1 TTTCTTTTAAGAA
* *
14245 TTTCTTTTGATAA
1 TTTCTTTTAAGAA
*
14258 TTTTATTTTAAGAA
1 -TTTCTTTTAAGAA
14272 -TTCTTTTA
1 TTTCTTTTA
14280 TACATTTCGT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 7 0.25
13 11 0.39
14 10 0.36
ACGTcount: A:0.27, C:0.06, G:0.06, T:0.60
Consensus pattern (13 bp):
TTTCTTTTAAGAA
Found at i:14273 original size:14 final size:14
Alignment explanation
Indices: 14230--14273 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
14220 GAAAAATTTT
14230 ATTTTCTTTTAAGA
1 ATTTTCTTTTAAGA
* *
14244 A-TTTCTTTTGATA
1 ATTTTCTTTTAAGA
*
14257 ATTTTATTTTAAGA
1 ATTTTCTTTTAAGA
14271 ATT
1 ATT
14274 CTTTTATACA
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.59
Consensus pattern (14 bp):
ATTTTCTTTTAAGA
Found at i:14286 original size:26 final size:27
Alignment explanation
Indices: 14230--14286 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
14220 GAAAAATTTT
*
14230 ATTTTCTTTTAAGAATTTCTTTTGATA
1 ATTTTATTTTAAGAATTTCTTTTGATA
14257 ATTTTATTTTAAGAA-TTCTTTT-ATA
1 ATTTTATTTTAAGAATTTCTTTTGATA
14282 CATTT
1 -ATTT
14287 CGTTTTCATC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 3 0.11
26 11 0.39
27 14 0.50
ACGTcount: A:0.28, C:0.07, G:0.05, T:0.60
Consensus pattern (27 bp):
ATTTTATTTTAAGAATTTCTTTTGATA
Found at i:14292 original size:26 final size:26
Alignment explanation
Indices: 14232--14292 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
14222 AAAATTTTAT
14232 TTTCTTTTAAGAATTTCTTTTGATAA
1 TTTCTTTTAAGAATTTCTTTTGATAA
*
14258 TTTTATTTTAAGAA-TTCTTTT-ATACA
1 -TTTCTTTTAAGAATTTCTTTTGATA-A
14284 TTTCGTTTT
1 TTTC-TTTT
14293 CATCAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
25 6 0.20
26 12 0.40
27 12 0.40
ACGTcount: A:0.25, C:0.08, G:0.07, T:0.61
Consensus pattern (26 bp):
TTTCTTTTAAGAATTTCTTTTGATAA
Found at i:17756 original size:19 final size:19
Alignment explanation
Indices: 17712--17767 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
17702 CTGCCAGTTT
**
17712 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
17732 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
17751 CATGTATCGATACAATG
1 CATGTATCGATACAATG
17768 TATCGATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:17770 original size:13 final size:13
Alignment explanation
Indices: 17752--17778 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
17742 TACAATGAAC
17752 ATGTATCGATACA
1 ATGTATCGATACA
17765 ATGTATCGATACA
1 ATGTATCGATACA
17778 A
1 A
17779 AGCAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:17793 original size:33 final size:32
Alignment explanation
Indices: 17733--17797 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
17723 ACAATTGTCC
*
17733 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCGATACAAAGAACATGTATCGATACA
*
17765 ATGTATCGATACAAAGCAGCATGTATCGATACA
1 ATGTATCGATACAAAG-AACATGTATCGATACA
17798 TCTGGGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.26
Consensus pattern (32 bp):
ATGTATCGATACAAAGAACATGTATCGATACA
Found at i:22361 original size:13 final size:13
Alignment explanation
Indices: 22343--22368 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
22333 TACAGCAAGT
22343 ATGTATCGATACA
1 ATGTATCGATACA
22356 ATGTATCGATACA
1 ATGTATCGATACA
22369 CAAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:24606 original size:21 final size:21
Alignment explanation
Indices: 24573--24617 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
24563 TTGCAAGTTG
*
24573 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
24595 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
24615 AAA
1 AAA
24618 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:28545 original size:13 final size:13
Alignment explanation
Indices: 28527--28565 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
28517 ACATTTTTCT
28527 TTGTATCGATACA
1 TTGTATCGATACA
28540 TTGTATCGATACA
1 TTGTATCGATACA
28553 TTGTATCGATACA
1 TTGTATCGATACA
28566 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:28729 original size:20 final size:20
Alignment explanation
Indices: 28686--28731 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
28676 AAATCTTTTG
28686 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
28707 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
28727 CAAAA
1 CAAAA
28732 CCAGTATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:31130 original size:13 final size:13
Alignment explanation
Indices: 31112--31137 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31102 TACAGCAAGT
31112 ATGTATCGATACA
1 ATGTATCGATACA
31125 ATGTATCGATACA
1 ATGTATCGATACA
31138 CAAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:36940 original size:32 final size:31
Alignment explanation
Indices: 36880--37098 Score: 182
Period size: 32 Copynumber: 7.0 Consensus size: 31
36870 GGTGCCATCA
* **** *
36880 ACTTGTGTGGGCTTTGAAAAAAAATGCCACAA
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCAC-G
* *
36912 ACTTGTGTGGGCTTTAAAGGGGGTTGCCAGCG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCA-CG
* *
36944 ACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCA-CG
*
36976 ACTTGTGTGGGCTTTGAATG-GGGTTGCTAGCG
1 ACTTGTGTGGGCTTTGAA-GAGGGTTGCCA-CG
* *
37008 ACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCA-CG
37040 ACTTGTGTGGGCTTT-AGAGAAGGG-TGCCACTG
1 ACTTGTGTGGGCTTTGA-AG-AGGGTTGCCAC-G
*
37072 AC-T-TGTGGGTTTTGAA-AGGG-TGCCACG
1 ACTTGTGTGGGCTTTGAAGAGGGTTGCCACG
37099 GAGTTGTGGA
Statistics
Matches: 156, Mismatches: 24, Indels: 19
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.01
28 10 0.06
30 10 0.06
31 4 0.03
32 125 0.80
33 6 0.04
ACGTcount: A:0.19, C:0.16, G:0.36, T:0.29
Consensus pattern (31 bp):
ACTTGTGTGGGCTTTGAAGAGGGTTGCCACG
Found at i:37024 original size:64 final size:64
Alignment explanation
Indices: 36912--37055 Score: 261
Period size: 64 Copynumber: 2.2 Consensus size: 64
36902 AATGCCACAA
36912 ACTTGTGTGGGCTTTAAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTAAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
* * *
36976 ACTTGTGTGGGCTTTGAATGGGGTTGCTAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTAAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
37040 ACTTGTGTGGGCTTTA
1 ACTTGTGTGGGCTTTA
37056 GAGAAGGGTG
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 76 1.00
ACGTcount: A:0.15, C:0.16, G:0.38, T:0.31
Consensus pattern (64 bp):
ACTTGTGTGGGCTTTAAAGGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
Found at i:37075 original size:64 final size:65
Alignment explanation
Indices: 36912--37078 Score: 254
Period size: 64 Copynumber: 2.6 Consensus size: 65
36902 AATGCCACAA
*
36912 ACTTGTGTGGGCTTTAAAG-GGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
1 ACTTGTGTGGGCTTTAGAGAGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
*
36976 ACTTGTGTGGGCTTT-GA-ATGGGGTTGCTAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACC
1 ACTTGTGTGGGCTTTAGAGA-GGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACC
37039 G
65 G
*
37040 ACTTGTGTGGGCTTTAGAGAAGGG-TGCCA-CTGACTTGTG
1 ACTTGTGTGGGCTTTAGAGAGGGGTTGCCAGC-GACTTGTG
37079 GGTTTTGAAA
Statistics
Matches: 94, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
63 2 0.02
64 86 0.91
65 5 0.05
66 1 0.01
ACGTcount: A:0.16, C:0.16, G:0.38, T:0.30
Consensus pattern (65 bp):
ACTTGTGTGGGCTTTAGAGAGGGGTTGCCAGCGACTTGTGTGGACTTTGGAGAGGGTTGCCACCG
Found at i:37191 original size:32 final size:28
Alignment explanation
Indices: 37045--39396 Score: 660
Period size: 27 Copynumber: 85.9 Consensus size: 28
37035 CACCGACTTG
* *
37045 TGTGGGCTTTAGAGAAGGGTGCCACTGACT
1 TGTGGGCTTTA-A-AAGGATGCCACTAACT
* * * ** *
37075 TGTGGGTTTTGAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
*
37103 TGTGGAC-TTAAAACGGATGCCACTAACT
1 TGTGGGCTTTAAAA-GGATGCCACTAACT
* * *
37131 TGTGGACTTTAAAAGGGTGTCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
37159 TGTGGGCTTTAAAAAAGAAGATGCCACTAACT
1 TGTGGGCTTT--AAAAG--GATGCCACTAACT
* * *
37191 TGTGGGCTTTTGAAAA-GATACCATTGACT
1 TGTGGGC-TTT-AAAAGGATGCCACTAACT
* * *
37220 TGTGGACTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
37248 TGTGAGCTTTGAAAGGGTGTCACTAA-T
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
37275 TCGTGGGCTTTGAAAGGATGTCACTGAC-
1 T-GTGGGCTTTAAAAGGATGCCACTAACT
* * *
37303 TGTGGACTTTGAAAGGGTGCCACTAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
37331 TGTGGGCTTTGCAAAGG-TGCCACTGACT
1 TGTGGGCTTT-AAAAGGATGCCACTAACT
* * * *
37359 TGTGAGC-TTAAAAGAATGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* * * ** *
37386 TGTGGTC-ATGAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
37413 TGTGGAC-TTAAAAGGATGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * ** * *
37440 TATAGAATTTAAAA-GATGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* * * *
37467 TGTGGAC-TTAAAAGGGTGCCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* * *
37494 TGTGGAC-TTAAAAGGGTGCCA-TGAAGT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* * ****
37521 TGTGGACTTTAAAAGGGTGCCACGGGGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * **
37549 TATGGAC-TTAAAAAGATGCCACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
37576 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
37603 TGTGGAC-TTAAAAGGATGCCACGAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * * *
37630 TGTGGACTTTAAAAGGGTACCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
37658 TGTGGAC-TTAAAAGGATACCAC-AGACT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * * ** *
37685 TCT-GGATTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
37712 TGTGGAC-TTAAAAAGATGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * *
37739 TGTGGAG--TTAAAAGGGTGCCACGAAGT
1 TGTGG-GCTTTAAAAGGATGCCACTAACT
* * * ** *
37766 TGTGGACTTTAAAAGGGTGTCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
37794 TGTGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * **
37822 TGTGGAC-TTAAAAGGATGCTACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
** *
37849 TGTGAAC-TTAAAA-GAGTGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGA-TGCCACTA-ACT
* ** *
37876 TGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
37903 TATGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ****
37931 TCTGGAC-TTAAAAGGATGCCACGGTGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * **
37958 TGTGGAC-TTAAAAGGATACCACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
37985 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* **
38012 TGTGGAC-TTAAAAGGATGCCACGCACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
38039 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
38066 TGTGGAC-TTAAAAAGATGCCACGAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * * *
38093 TGTGGACTTTAAAAGGGTACCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
38121 TGTGGAC-TTAAAAGGATACCAC-AGACT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * * ** *
38148 TCT-GGATTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
38175 TGTGGAC-TTAAAAAGATGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * *
38202 TGTGGAG--TTAAAAGGGTGCCACGAAGT
1 TGTGG-GCTTTAAAAGGATGCCACTAACT
* * * ** *
38229 TGTGGACTTTAAAAGGGTGTCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
38257 TGTGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * **
38285 TGTGGAC-TTAAAAGGATGCTACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
38312 TGTGGAC-TTAAAA-GAGTGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGA-TGCCACTA-ACT
* ** *
38339 TGTGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
38366 TGTGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ****
38394 TCTGGAC-TTAAAAGGATGCCACGGTGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * **
38421 TGTGGAC-TTAAAAGGATACCACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
38448 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* **
38475 TGTGGAC-TTAAAAGGATGCCACGCACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
38502 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* **
38529 TGTGGAC-TTAAAAGGATGCCACGCACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
38556 TGTGGAC-TTAATAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * ** *
38583 TGTGGTC-ATGAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
38610 TATGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** ** *
38637 TATAGAATTTAAAA-GATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
38664 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
** * * *
38691 TGTGAAC-TTAAAA-GAGCGCCACGAAGT
1 TGTGGGCTTTAAAAGGA-TGCCACTAACT
* * *
38718 TGTGGACTTTAAAAGGGTGCCACGAACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ****
38746 TCTGGAC-TTAAAAGGATGCCACGGTGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
38773 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * * *
38800 TGTGGAC-TTAAAAGGGTGTCA-TGGAGT
1 TGTGGGCTTTAAAAGGATGCCACT-AACT
* * ** *
38827 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
38855 TATGGAC-TTAAAAGGATGCCAC-AGACT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * * *
38882 TGTGGAC-TTAAAAGGGTGCCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * *
38909 TGTGGACTTAAAAAGG-TGCCACAAAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * * ** *
38936 TGTGGAC-TTAAAAGGGTACCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * *
38963 TGTGGACTTTAAAAGGTTACCAC-AGACT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
*
38991 TGTGGAC-TTAAAAGGATGCCAC-AGACT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * *
39018 TGTGGAC-TTAAAAGGGTGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* *
39045 TGTGGAC-TTAAAAGGATGCCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * *
39072 TGTGGAG--TTAAAAGGGTGCCACGAAGT
1 TGTGG-GCTTTAAAAGGATGCCACTAACT
* * * *
39099 TGTGGACTTTAAAAGGGTGTCAC-AGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* ** *
39127 TGTGGACTTTAAAACGG-TGTTA-TGGACT
1 TGTGGGCTTTAAAA-GGATGCCACT-AACT
* **
39155 TGTGGAC-TTAAAA-GAGTGCCAC-AGAGG
1 TGTGGGCTTTAAAAGGA-TGCCACTA-ACT
* *
39182 TGTGGAC-TTAAAAGGATGCCA-TAGAGT
1 TGTGGGCTTTAAAAGGATGCCACTA-ACT
* * **
39209 TGTGGACTTTAAAAGGGTGCCACGCACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
39237 TATGGAC-TTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
39264 TGTGGAC-TTAAAAGGATACCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
39291 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* * ** *
39318 TGTGGAC-TTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* **
39345 TGTGGAC-TTAAAAGGATGCCACGGACT
1 TGTGGGCTTTAAAAGGATGCCACTAACT
* *
39372 TATGGACTTTAAAAGGAATGCCACT
1 TGTGGGCTTTAAAAGG-ATGCCACT
39397 GAATCGTGGA
Statistics
Matches: 1951, Mismatches: 287, Indels: 169
0.81 0.12 0.07
Matches are distributed among these distances:
25 1 0.00
26 33 0.02
27 1314 0.67
28 526 0.27
29 38 0.02
30 14 0.01
32 22 0.01
33 3 0.00
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (28 bp):
TGTGGGCTTTAAAAGGATGCCACTAACT
Found at i:37220 original size:29 final size:28
Alignment explanation
Indices: 37066--37367 Score: 137
Period size: 28 Copynumber: 10.6 Consensus size: 28
37056 GAGAAGGGTG
* * * *
37066 CCACTGACTTGTGGGTTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGATA
* * * *
37094 CCACGGAGTTGTGGAC-TT-AAAACGGATG
1 CCACTGACTTGTGGGCTTTGAAAA--GATA
* * * *
37122 CCACTAACTTGTGGACTTT-AAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAA-GATA
* * * *
37150 TCACTAACTTGTGGGCTTTAAAAAAGAAGATG
1 CCACTGACTTGTGGGCTTT---GAA-AAGATA
*
37182 CCACTAACTTGTGGGCTTTTGAAAAGATA
1 CCACTGACTTGTGGGC-TTTGAAAAGATA
* * * *
37211 CCATTGACTTGTGGACTTTGAAAGGATG
1 CCACTGACTTGTGGGCTTTGAAAAGATA
* * * *
37239 CCACTGACTTGTGAGCTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGATA
* * * *
37267 TCACT-AATTCGTGGGCTTTGAAAGGATG
1 CCACTGACTT-GTGGGCTTTGAAAAGATA
* * * * *
37295 TCACTGAC-TGTGGACTTTGAAAGGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGATA
* * * *
37322 CCACTAACTTGTGGGCTTTGCAAAGGTG
1 CCACTGACTTGTGGGCTTTGAAAAGATA
*
37350 CCACTGACTTGTGAGCTT
1 CCACTGACTTGTGGGCTT
37368 AAAAGAATGC
Statistics
Matches: 223, Mismatches: 39, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
26 3 0.01
27 27 0.12
28 141 0.63
29 25 0.11
30 2 0.01
32 20 0.09
33 5 0.02
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.29
Consensus pattern (28 bp):
CCACTGACTTGTGGGCTTTGAAAAGATA
Found at i:37223 original size:117 final size:116
Alignment explanation
Indices: 37064--37285 Score: 297
Period size: 117 Copynumber: 1.9 Consensus size: 116
37054 TAGAGAAGGG
* * * * *
37064 TGCCACTGACTTGTGGGTTTTGAAAGGGTGCCACGGAGTTGTGGAC-TTAAAACGGATGCCACTA
1 TGCCACTAACTTGTGGGTTTTGAAAAGATACCACGGACTTGTGGACTTTAAAA-GGATGCCACTA
37128 ACTTGTG-GACTTTAAAAGGGTGTCACTAACTT-GTGGGCTTTAAAAAAGAAGA
65 ACTTGTGAG-CTTTAAAAGGGTGTCACTAA-TTCGTGGGCTTTAAAAAAGAAGA
** * *
37180 TGCCACTAACTTGTGGGCTTTTGAAAAGATACCATTGACTTGTGGACTTTGAAAGGATGCCACTG
1 TGCCACTAACTTGTGGG-TTTTGAAAAGATACCACGGACTTGTGGACTTTAAAAGGATGCCACTA
*
37245 ACTTGTGAGCTTTGAAAGGGTGTCACTAATTCGTGGGCTTT
65 ACTTGTGAGCTTTAAAAGGGTGTCACTAATTCGTGGGCTTT
37286 GAAAGGATGT
Statistics
Matches: 92, Mismatches: 10, Indels: 7
0.84 0.09 0.06
Matches are distributed among these distances:
116 18 0.20
117 68 0.74
118 6 0.07
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (116 bp):
TGCCACTAACTTGTGGGTTTTGAAAAGATACCACGGACTTGTGGACTTTAAAAGGATGCCACTAA
CTTGTGAGCTTTAAAAGGGTGTCACTAATTCGTGGGCTTTAAAAAAGAAGA
Found at i:37388 original size:27 final size:27
Alignment explanation
Indices: 37343--39409 Score: 2309
Period size: 27 Copynumber: 76.0 Consensus size: 27
37333 TGGGCTTTGC
* *
37343 AAAGG-TGCCACTGACTTGT-GAGCTTA
1 AAAGGATGCCACGGAGTTGTGGA-CTTA
* * * * *
37369 AAAGAATGCCATGGAGTTGTGGTCATG
1 AAAGGATGCCACGGAGTTGTGGACTTA
37396 AAAGGATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * * *
37423 AAAGGATGCCACAGAGTTATAGAATTTA
1 AAAGGATGCCACGGAGTTGT-GGACTTA
*
37451 AAA-GATGCCATGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
37477 AAAGGGTGCCATGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
37504 AAAGGGTGCCATGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
37532 AAAGGGTGCCACGGGGTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
37559 AAAAGATGCCACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* **
37586 AAAGGGTGCCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
37613 AAAGGATGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * **
37641 AAAGGGTACCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * * * *
37668 AAAGGATACCACAGACTTCTGGATTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
37695 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
37722 AAAAGATGCCACAGAGTTGTGGAGTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
37749 AAAGGGTGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* *
37777 AAAGGGTGTCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
37805 AAAGGGTGCCACGAACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
37832 AAAGGATGCTACGGACTTGTGAACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
37859 AAA-GAGTGCCACAGAGTTGTGGACTTA
1 AAAGGA-TGCCACGGAGTTGTGGACTTA
*
37886 AAAGGATGCCACGGAGTTATGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
37914 AAAGGGTGCCACGAACTTCTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
37941 AAAGGATGCCACGGTGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
37968 AAAGGATACCACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
37995 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38022 AAAGGATGCCACGCACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
38049 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38076 AAAAGATGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * **
38104 AAAGGGTACCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * * * *
38131 AAAGGATACCACAGACTTCTGGATTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
38158 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
38185 AAAAGATGCCACAGAGTTGTGGAGTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38212 AAAGGGTGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* *
38240 AAAGGGTGTCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
38268 AAAGGGTGCCACGAACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38295 AAAGGATGCTACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
38322 AAA-GAGTGCCACAGAGTTGTGGACTTA
1 AAAGGA-TGCCACGGAGTTGTGGACTTA
38349 AAAGGATGCCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
38377 AAAGGGTGCCACGAACTTCTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
38404 AAAGGATGCCACGGTGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38431 AAAGGATACCACGGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
38458 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38485 AAAGGATGCCACGCACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
38512 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38539 AAAGGATGCCACGCACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * * *
38566 ATAGGATGCCACGGAGTTGTGGTCATG
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
38593 AAAGGATGCCACGGAGTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
38620 AAAGGATGCCACGGAGTTATAGAATTTA
1 AAAGGATGCCACGGAGTTGT-GGACTTA
38648 AAA-GATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38674 AAAGGGTGCCACGGAGTTGTGAACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38701 AAA-GAGCGCCACGAAGTTGTGGACTTTA
1 AAAGGA-TGCCACGGAGTTGTGGAC-TTA
* * * *
38729 AAAGGGTGCCACGAACTTCTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
38756 AAAGGATGCCACGGTGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* **
38783 AAAGGGTGCCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* * *
38810 AAAGGGTGTCATGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* *
38838 AAAGGGTGCCACGGAGTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38865 AAAGGATGCCACAGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* **
38892 AAAGGGTGCCACAAAGTTGTGGACTTAA
1 AAAGGATGCCACGGAGTTGTGGACTT-A
**
38920 AAAGG-TGCCACAAAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
38946 AAAGGGTACCACGGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
38974 AAAGGTTACCACAGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
39001 AAAGGATGCCACAGACTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
39028 AAAGGGTGCCACAGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
39055 AAAGGATGCCACAGAGTTGTGGAGTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
39082 AAAGGGTGCCACGAAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
39110 AAAGGGTGTCACAGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
** * *
39138 AAACGG-TGTTATGGACTTGTGGACTTA
1 AAA-GGATGCCACGGAGTTGTGGACTTA
* *
39165 AAA-GAGTGCCACAGAGGTGTGGACTTA
1 AAAGGA-TGCCACGGAGTTGTGGACTTA
**
39192 AAAGGATGCCATAGAGTTGTGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * * *
39220 AAAGGGTGCCACGCACTTATGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
39247 AAAGGATGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
39274 AAAGGATACCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
39301 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
*
39328 AAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAGGATGCCACGGAGTTGTGGACTTA
* *
39355 AAAGGATGCCACGGACTTATGGACTTTA
1 AAAGGATGCCACGGAGTTGTGGAC-TTA
* * *
39383 AAAGGAATGCCACTGAATCGTGGACTT
1 AAAGG-ATGCCACGGAGTTGTGGACTT
39410 TGAAAGGTTA
Statistics
Matches: 1748, Mismatches: 261, Indels: 62
0.84 0.13 0.03
Matches are distributed among these distances:
25 1 0.00
26 31 0.02
27 1308 0.75
28 390 0.22
29 18 0.01
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (27 bp):
AAAGGATGCCACGGAGTTGTGGACTTA
Found at i:37588 original size:109 final size:108
Alignment explanation
Indices: 37343--39409 Score: 2375
Period size: 109 Copynumber: 19.0 Consensus size: 108
37333 TGGGCTTTGC
* * ** * * * * *
37343 AAAGG-TGCCACTGACTTGT-GAGCTTAAAAGAATGCCATGGAGTTGTGGTCATGAAAGGATGCC
1 AAAGGATGCCACGGAGTTGTGGA-CTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * * *
37406 ACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTATAGAATTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT-GGACTTA
* *
37451 AAA-GATGCCATGGAGTTGTGGACTTAAAAGGGTGCCATGGAGTTGTGGACTTAAAAGGGTGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * * *
37515 TGAAGTTGTGGACTTTAAAAGGGTGCCACGGGGTTATGGACTTA
66 CGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTA
* * ** *
37559 AAAAGATGCCACGGACTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTAAAAGGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * **
37624 CGAAGTTGTGGACTTTAAAAGGGTACCACAAAGTTGTGGACTTA
66 CGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * * * *
37668 AAAGGATACCACAGACTTCTGGATTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * *
37733 CAGAGTTGTGGAGTTAAAAGGGTGCCACGAAGTTGTGGACTTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* * * * * *
37777 AAAGGGTGTCACGGAGTTGTGGACTTTAAAAGGGTGCCACGAACTTGTGGACTTAAAAGGATGCT
1 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * *
37842 ACGGACTTGTGAACTTAAAA-GAGTGCCACAGAGTTGTGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGA-TGCCACGGAGTTGTGGACTTA
* * * * *
37886 AAAGGATGCCACGGAGTTATGGACTTTAAAAGGGTGCCACGAACTTCTGGACTTAAAAGGATGCC
1 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
* * *
37951 ACGGTGTTGTGGACTTAAAAGGATACCACGGACTTGTGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * *
37995 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACGCACTTGTGGACTTAAAAGGGTGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* *
38060 CGGAGTTGTGGACTTAAAAAGATGCCACGAAGTTGTGGACTTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* * ** * * * * * *
38104 AAAGGGTACCACAAAGTTGTGGACTTAAAAGGATACCACAGACTTCTGGATTTAAAAGGGTGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * *
38169 CGGAGTTGTGGACTTAAAAAGATGCCACAGAGTTGTGGAGTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * *
38212 AAAGGGTGCCACGAAGTTGTGGACTTTAAAAGGGTGTCACGGAGTTGTGGACTTTAAAAGGGTGC
1 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
* * * *
38277 CACGAACTTGTGGACTTAAAAGGATGCTACGGACTTGTGGACTTA
64 CACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* *
38322 AAA-GAGTGCCACAGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGGTGC
1 AAAGGA-TGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
* * * *
38386 CACGAACTTCTGGACTTAAAAGGATGCCACGGTGTTGTGGACTTA
64 CACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * *
38431 AAAGGATACCACGGACTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * *
38496 CGCACTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * * * * *
38539 AAAGGATGCCACGCACTTGTGGACTTAATAGGATGCCACGGAGTTGTGGTCATGAAAGGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * *
38604 CGGAGTTATGGACTTAAAAGGATGCCACGGAGTTATAGAATTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGT-GGACTTA
* * *
38648 AAA-GATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGAACTTAAAAGAGCGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * * *
38712 CGAAGTTGTGGACTTTAAAAGGGTGCCACGAACTTCTGGACTTA
66 CGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTA
* ** *
38756 AAAGGATGCCACGGTGTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTAAAAGGGTGTCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * *
38821 TGGAGTTGTGGACTTTAAAAGGGTGCCACGGAGTTATGGACTTA
66 CGGAGTTGTGGAC-TTAAAAGGATGCCACGGAGTTGTGGACTTA
* * ** *
38865 AAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCACAAAGTTGTGGACTTAAAAAGGTGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
** * *
38930 CAAAGTTGTGGACTTAAAAGGGTACCACGGAGTTGTGGACTTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGAC-TTA
* * * * * * *
38974 AAAGGTTACCACAGACTTGTGGACTTAAAAGGATGCCACAGACTTGTGGACTTAAAAGGGTGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * *
39039 CAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGAGTTA
66 CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* * * * * *
39082 AAAGGGTGCCACGAAGTTGTGGACTTTAAAAGGGTGTCACAGAGTTGTGGACTTTAAAACGGTGT
1 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGAC-TTAAAAGGGTGC
* * * * *
39147 TATGGACTTGTGGACTTAAAA-GAGTGCCACAGAGGTGTGGACTTA
64 CACGGAGTTGTGGACTTAAAAGGA-TGCCACGGAGTTGTGGACTTA
** * * * *
39192 AAAGGATGCCATAGAGTTGTGGACTTTAAAAGGGTGCCACGCACTTATGGACTTAAAAGGATGCC
1 AAAGGATGCCACGGAGTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCC
*
39257 ACGGAGTTGTGGACTTAAAAGGATACCACGGAGTTGTGGACTTA
65 ACGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
* *
39301 AAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGATGCCA
1 AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
* * * * *
39366 CGGACTTATGGACTTTAAAAGGAATGCCACTGAATCGTGGACTT
66 CGGAGTTGTGGAC-TTAAAAGG-ATGCCACGGAGTTGTGGACTT
39410 TGAAAGGTTA
Statistics
Matches: 1698, Mismatches: 238, Indels: 44
0.86 0.12 0.02
Matches are distributed among these distances:
107 1 0.00
108 497 0.29
109 951 0.56
110 249 0.15
ACGTcount: A:0.31, C:0.15, G:0.30, T:0.24
Consensus pattern (108 bp):
AAAGGATGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCA
CGGAGTTGTGGACTTAAAAGGATGCCACGGAGTTGTGGACTTA
Found at i:40678 original size:13 final size:13
Alignment explanation
Indices: 40660--40684 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40650 ATTACTCAAA
40660 TGTATCGATACAT
1 TGTATCGATACAT
40673 TGTATCGATACA
1 TGTATCGATACA
40685 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:40786 original size:52 final size:52
Alignment explanation
Indices: 40693--40816 Score: 207
Period size: 52 Copynumber: 2.4 Consensus size: 52
40683 CACTGATCTT
*
40693 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATT-AAA
40744 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
40796 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
40817 CTTTTCATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 19 0.28
52 47 0.68
53 3 0.04
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:48296 original size:22 final size:22
Alignment explanation
Indices: 48270--48325 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
48260 TTTTTCTTTG
48270 TTTCT-ATTTCTTCTCTCTTTTT
1 TTTCTCATTT-TTCTCTCTTTTT
* *
48292 TTTCTCCTTTTTTTCTCTTTTT
1 TTTCTCATTTTTCTCTCTTTTT
* *
48314 TTTTTCTTTTTT
1 TTTCTCATTTTT
48326 TTAGTTGAAC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 26 0.90
23 3 0.10
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCTCATTTTTCTCTCTTTTT
Found at i:48327 original size:11 final size:11
Alignment explanation
Indices: 48283--48327 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
48273 CTATTTCTTC
48283 TCTCTTTTTTT
1 TCTCTTTTTTT
*
48294 TCTCCTTTTTT
1 TCTCTTTTTTT
48305 TCTCTTTTTTT
1 TCTCTTTTTTT
*
48316 TTTCTTTTTTT
1 TCTCTTTTTTT
48327 T
1 T
48328 AGTTGAACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTCTTTTTTT
Found at i:50206 original size:20 final size:21
Alignment explanation
Indices: 50181--50229 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
50171 GCACTCGTTA
50181 GATGAAAAGACATACTT-TTG
1 GATGAAAAGACATACTTGTTG
**
50201 GATGAAAAGATGTACTTGTTG
1 GATGAAAAGACATACTTGTTG
*
50222 GACGAAAA
1 GATGAAAA
50230 AAATTCAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.41, C:0.08, G:0.24, T:0.27
Consensus pattern (21 bp):
GATGAAAAGACATACTTGTTG
Found at i:53479 original size:8 final size:8
Alignment explanation
Indices: 53421--53473 Score: 52
Period size: 8 Copynumber: 6.4 Consensus size: 8
53411 TTGCTTATTA
*
53421 TCTCTTCG
1 TCTCTTCT
53429 TCTCTTCT
1 TCTCTTCT
*
53437 TCTCTTTT
1 TCTCTTCT
* *
53445 TTTCCTTTT
1 TCT-CTTCT
53454 TCTCTTCT
1 TCTCTTCT
53462 TCTTCTTCT
1 TC-TCTTCT
53471 TCT
1 TCT
53474 TCTCTTGCTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
8 23 0.61
9 15 0.39
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (8 bp):
TCTCTTCT
Found at i:55758 original size:20 final size:20
Alignment explanation
Indices: 55733--55786 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
55723 CTACCACTGT
* *
55733 TTGTATCGATACATGGTCCA
1 TTGTATCGATACATGATCAA
*
55753 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATCAA
55773 TTGTATCGATACAT
1 TTGTATCGATACAT
55787 TGCTTGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.15, G:0.19, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATCAA
Found at i:58018 original size:21 final size:20
Alignment explanation
Indices: 57984--58026 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
57974 TATTAAAAAG
*
57984 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAACAA-GAA
58005 TTAGCTAA-GAAAAACAAGAA
1 TTAGCTAATG-AAAACAAGAA
58025 TT
1 TT
58027 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (20 bp):
TTAGCTAATGAAAACAAGAA
Found at i:58025 original size:20 final size:21
Alignment explanation
Indices: 57984--58026 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
57974 TATTAAAAAG
*
57984 TTAGCTAATGAAAATAATGAA
1 TTAGCTAATGAAAATAAAGAA
58005 TTAGCTAA-GAAAA-ACAAGAA
1 TTAGCTAATGAAAATA-AAGAA
58025 TT
1 TT
58027 TGCATGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 11 0.55
21 8 0.40
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (21 bp):
TTAGCTAATGAAAATAAAGAA
Found at i:60368 original size:33 final size:34
Alignment explanation
Indices: 60305--60370 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
60295 TATTACAAGC
*
60305 AATGTATCGATACAATTTCATCATGTATCGATAT
1 AATGTATCGATACAATTTCACCATGTATCGATAT
60339 AATGTATCGATAC-ATTGTC-CCATGTATCGATA
1 AATGTATCGATACAATT-TCACCATGTATCGATA
60371 CAAATAGTGG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 15 0.50
34 15 0.50
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (34 bp):
AATGTATCGATACAATTTCACCATGTATCGATAT
Found at i:62961 original size:13 final size:13
Alignment explanation
Indices: 62942--62980 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
62932 AAATAGTACC
62942 CAATGTATCGATA
1 CAATGTATCGATA
* *
62955 TAATGTATTGATA
1 CAATGTATCGATA
*
62968 CATTGTATCGATA
1 CAATGTATCGATA
62981 AAGGAATGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:67531 original size:3 final size:3
Alignment explanation
Indices: 67523--67547 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
67513 TCCGAGTCAC
67523 CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT C
67548 TTCCTCTTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:68486 original size:13 final size:13
Alignment explanation
Indices: 68468--68524 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
68458 CATAAAGTGT
68468 TGTATCGATACAA
1 TGTATCGATACAA
68481 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
68496 GTGTTGTACCGATACAA
1 ----TGTATCGATACAA
68513 TGTATCGATACA
1 TGTATCGATACA
68525 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:68503 original size:32 final size:32
Alignment explanation
Indices: 68450--68545 Score: 165
Period size: 32 Copynumber: 3.0 Consensus size: 32
68440 CAATGATTTA
68450 TATCGATACATAAAGTGTTGTATCGATACAATG
1 TATCGATACAT-AAGTGTTGTATCGATACAATG
*
68483 TATCGATACATAAGTGTTGTACCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATG
*
68515 TATCGATACATAAGTTTTGTATCGATACAAT
1 TATCGATACATAAGTGTTGTATCGATACAAT
68546 TTAAGCTACT
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 49 0.82
33 11 0.18
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATG
Found at i:68537 original size:19 final size:18
Alignment explanation
Indices: 68450--68543 Score: 73
Period size: 19 Copynumber: 5.6 Consensus size: 18
68440 CAATGATTTA
68450 TATCGATACATAAAGTGTTG
1 TATCGATACAT-AAGT-TTG
68470 TATCGATAC--AA---TG
1 TATCGATACATAAGTTTG
68483 TATCGATACATAAGTGTTG
1 TATCGATACATAAGT-TTG
*
68502 TACCGATAC--AA---TG
1 TATCGATACATAAGTTTG
68515 TATCGATACATAAGTTTTG
1 TATCGATACATAAG-TTTG
68534 TATCGATACA
1 TATCGATACA
68544 ATTTAAGCTA
Statistics
Matches: 60, Mismatches: 2, Indels: 25
0.69 0.02 0.29
Matches are distributed among these distances:
13 21 0.35
15 4 0.07
17 4 0.07
19 22 0.37
20 9 0.15
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (18 bp):
TATCGATACATAAGTTTG
Found at i:68604 original size:13 final size:13
Alignment explanation
Indices: 68586--68610 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
68576 ATTACTCAAA
68586 TGTATCGATACAT
1 TGTATCGATACAT
68599 TGTATCGATACA
1 TGTATCGATACA
68611 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:68663 original size:52 final size:51
Alignment explanation
Indices: 68599--68747 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
68589 ATCGATACAT
**
68599 TGTATCGATACACTGATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
68651 TGTATCGATACACTA-CAAAATATATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATC--AATGTATCGATACATGCAGGCAAATTTGCCCAGA
*
68703 TGTATCGATACACTATAAAATGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACACTAT-CAATGTATCGATACATGCAGGCAAATTT
68748 TCATATTTCG
Statistics
Matches: 88, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
50 1 0.01
51 1 0.01
52 86 0.98
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (51 bp):
TGTATCGATACACTATCAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Done.