Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007912.1 Hibiscus syriacus cultivar Beakdansim tig00110313_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: 1361188
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
File 1 of 6
Found at i:2942 original size:26 final size:27
Alignment explanation
Indices: 2913--2980 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
2903 AATCGAAACC
2913 TTTTGCATTTGCATTTACA-TTCACAT
1 TTTTGCATTTGCATTTACATTTCACAT
* * * **
2939 TTTTACGTTTGTATTTACATTTTCATTT
1 TTTTGCATTTGCATTTACA-TTTCACAT
2967 TTTTGCATTTGCAT
1 TTTTGCATTTGCAT
2981 CTTTGCATAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 16 0.50
28 16 0.50
ACGTcount: A:0.19, C:0.15, G:0.09, T:0.57
Consensus pattern (27 bp):
TTTTGCATTTGCATTTACATTTCACAT
Found at i:5413 original size:5 final size:5
Alignment explanation
Indices: 5397--5453 Score: 63
Period size: 5 Copynumber: 12.6 Consensus size: 5
5387 TCATCCATCA
*
5397 AAAAG -AAA- AAAAG AAAAG AAAAG AAAA- AAGA- AAAAG -AAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG
5442 -AAAG AAAAG AAA
1 AAAAG AAAAG AAA
5454 TAAAATGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 20 0.44
5 25 0.56
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:5420 original size:18 final size:18
Alignment explanation
Indices: 5397--5453 Score: 82
Period size: 17 Copynumber: 3.2 Consensus size: 18
5387 TCATCCATCA
5397 AAAAGAAAAAAAGAAAAG
1 AAAAGAAAAAAAGAAAAG
5415 AAAAG-AAAAAAGAAAA-
1 AAAAGAAAAAAAGAAAAG
5431 AGAAAGAAAAGAAAGAAAAG
1 A-AAAGAAAA-AAAGAAAAG
5451 AAA
1 AAA
5454 TAAAATGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
16 1 0.03
17 15 0.43
18 8 0.23
19 10 0.29
20 1 0.03
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAAGAAAAG
Found at i:5442 original size:9 final size:9
Alignment explanation
Indices: 5398--5463 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
5388 CATCCATCAA
5398 AAAGAAAA-
1 AAAGAAAAG
5406 AAAGAAAAG
1 AAAGAAAAG
5415 AAA-AGAAA-
1 AAAGA-AAAG
5423 AAAGAAAAAG
1 AAAG-AAAAG
5433 AAAGAAAAG
1 AAAGAAAAG
5442 AAAGAAAAG
1 AAAGAAAAG
*
5451 AAATAAAATG
1 AAAGAAAA-G
5461 AAA
1 AAA
5464 TTGAATCAAG
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
8 12 0.24
9 30 0.59
10 9 0.18
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:7023 original size:28 final size:28
Alignment explanation
Indices: 6983--7040 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
6973 GTAATCCAAG
6983 TGGGGCATCTTGAAGGCTCACA-TCAGCA
1 TGGGGCATCTTGAAGGCTCACACT-AGCA
7011 TGGGGCATCTTGAAGGCTCACACTAGCA
1 TGGGGCATCTTGAAGGCTCACACTAGCA
7039 TG
1 TG
7041 AAAAGGTTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.22
Consensus pattern (28 bp):
TGGGGCATCTTGAAGGCTCACACTAGCA
Found at i:8394 original size:40 final size:40
Alignment explanation
Indices: 8337--8963 Score: 809
Period size: 40 Copynumber: 15.8 Consensus size: 40
8327 ATATGGAGGA
**
8337 TTTATCTCACTGGAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * *
8377 TTTATCTCATTCAAGATTGTTTTTCCTTGAAACATAAAAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * * * *
8417 TTTATTTCATTTAAAATTATTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * * * *
8457 TTTATTTCATTGAAGATTGTTTTTCTTTGAAACAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
8497 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
8537 TTTATCTCACTCAAGATTATTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
8577 TTTATCTCACTCAAGATTGTTTTTTCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
8617 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACGGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
8657 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
*
8697 TTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* *
8737 TTTATCTCGCTCAAGATTG-TTTTCCCTGAAACAGAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* *
8776 TTTATCTCGCTCAAGATTGTTTTTCCTTGAAACAGAATAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
** * *
8816 TTTATCTTGCTCAAGATTGTTTTTCCTTAAAACAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* ** * * * * *
8856 TTTATCTCGCTTGAGATAG-TTTCCCTCGAAATAAAAGAT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* ** * *
8895 TTTATCTCGCTTTAGATAG-TTTCCCTTGAAAC--AA-AT
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
* * * *
8931 TTTGTCTCACTTAAGATAG-TTTCCCTTGAAACA
1 TTTATCTCACTCAAGATTGTTTTTCCTTGAAACA
8964 AGTTTTGTCT
Statistics
Matches: 536, Mismatches: 49, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
36 31 0.06
37 2 0.00
39 83 0.15
40 420 0.78
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (40 bp):
TTTATCTCACTCAAGATTGTTTTTCCTTGAAACAGAAGAT
Found at i:8578 original size:20 final size:20
Alignment explanation
Indices: 8516--8579 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
8506 CTCAAGATTG
8516 TTTTTCCTTGAAACAGAAGA
1 TTTTTCCTTGAAACAGAAGA
* ** **
8536 TTTTAT-C-TCACTCAAGATTA
1 TTTT-TCCTTGAAAC-AGAAGA
8556 TTTTTCCTTGAAACAGAAGA
1 TTTTTCCTTGAAACAGAAGA
8576 TTTT
1 TTTT
8580 ATCTCACTCA
Statistics
Matches: 30, Mismatches: 10, Indels: 8
0.62 0.21 0.17
Matches are distributed among these distances:
19 4 0.13
20 22 0.73
21 4 0.13
ACGTcount: A:0.31, C:0.16, G:0.11, T:0.42
Consensus pattern (20 bp):
TTTTTCCTTGAAACAGAAGA
Found at i:8695 original size:23 final size:23
Alignment explanation
Indices: 8669--8737 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 23
8659 TATCTCACTC
8669 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
* * **
8692 AAGA-T-TTTAT-CTCG---CTC
1 AAGATTGTTTTTCCTTGAAACAG
8709 AAGATTGTTTTTCCTTGAAACAG
1 AAGATTGTTTTTCCTTGAAACAG
8732 AAGATT
1 AAGATT
8738 TTATCTCGCT
Statistics
Matches: 32, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
17 5 0.16
18 1 0.03
19 4 0.12
20 6 0.19
21 4 0.12
22 1 0.03
23 11 0.34
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (23 bp):
AAGATTGTTTTTCCTTGAAACAG
Found at i:8838 original size:20 final size:20
Alignment explanation
Indices: 8775--8838 Score: 51
Period size: 20 Copynumber: 3.2 Consensus size: 20
8765 AAACAGAAGA
*
8775 TTTTATCTCGCTCAAGATTG
1 TTTTATCTTGCTCAAGATTG
** * *
8795 TTTT-TCCTTG-AAACAGAATA
1 TTTTAT-CTTGCTCA-AGATTG
8815 TTTTATCTTGCTCAAGATTG
1 TTTTATCTTGCTCAAGATTG
8835 TTTT
1 TTTT
8839 TCCTTAAAAC
Statistics
Matches: 31, Mismatches: 9, Indels: 8
0.65 0.19 0.17
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.23, C:0.16, G:0.12, T:0.48
Consensus pattern (20 bp):
TTTTATCTTGCTCAAGATTG
Found at i:9106 original size:133 final size:132
Alignment explanation
Indices: 8893--9131 Score: 300
Period size: 133 Copynumber: 1.8 Consensus size: 132
8883 GAAATAAAAG
* * *
8893 ATTTTATCTCGCTTTAGATAGTTTCCCTTGAAACAAATTTTGTCTCACTTAAGATAGTTTCCCTT
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACTTAAGATAGTTTCCCTT
* * * *
8958 GAAACAAGTTTTGTCTCCCTTGAAATAGTTTCTCTTGAAAATTTTGAGAACATTTCCCTTGAAAC
66 AAAACAAGATTTGTCTCACTTGAAATAGTTTCTCTTAAAAATTTTGAGAACATTTCCCTTGAAAC
9023 GA
131 GA
* * * * * **
9025 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAGAGTTTTGTCTCCCTTAAGATGGTTTTTCT
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACA-AATTTTGTCTCACTTAAGATAGTTTCCCT
* * *
9090 TAAAACCAA-ATTTGTCTCACTTGAGATGGTTTTTCTTAAAAA
65 TAAAA-CAAGATTTGTCTCACTTGAAATAGTTTCTCTTAAAAA
9132 CCCTTGAGAC
Statistics
Matches: 88, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
132 30 0.34
133 55 0.62
134 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.14, T:0.41
Consensus pattern (132 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCACTTAAGATAGTTTCCCTT
AAAACAAGATTTGTCTCACTTGAAATAGTTTCTCTTAAAAATTTTGAGAACATTTCCCTTGAAAC
GA
Found at i:9147 original size:61 final size:61
Alignment explanation
Indices: 9092--9416 Score: 328
Period size: 61 Copynumber: 5.4 Consensus size: 61
9082 GTTTTTCTTA
* *
9092 AAACCAAATTTGTCTCACTTGAGATGGTTTTTCTTAAAAACCCTTGAGACAGTTTTCCTTTG
1 AAACAAAATTTATCTCACTTGAGATGGTTTTTCTT-AAAACCCTTGAGACAGTTTTCCTTTG
* ** * *** * *
9154 AAAC--AA-GT-T-T---TTGAGACAGTTTCTCTTGAAACAAGTTTTTGAGACAATTTTCCTTCG
1 AAACAAAATTTATCTCACTTGAGATGGTTTTTCTT--AA-AA-CCCTTGAGACAGTTTTCCTTTG
* *
9211 AAATAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTGCTTTG
1 AAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTCCTTTG
* * * *
9272 AAACAAAATTTATCTCAATTAATATGGTTTTTCTTAAAACCCTTGAGAC-GATTTTTCTTTG
1 AAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAG-TTTTCCTTTG
* * * *
9333 AAATAAAATTTATCTCATTTGAGATGGTTTTTCTTAAAA-CCTTGAGACAATTTTCCTTCG
1 AAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTCCTTTG
*
9393 AAGCAAAATTTATCTCACTTGAGA
1 AAACAAAATTTATCTCACTTGAGA
9417 GAGCTTCTCT
Statistics
Matches: 215, Mismatches: 35, Indels: 28
0.77 0.13 0.10
Matches are distributed among these distances:
54 14 0.07
55 3 0.01
56 2 0.01
57 21 0.10
58 1 0.00
59 3 0.01
60 42 0.20
61 106 0.49
62 7 0.03
63 2 0.01
65 14 0.07
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (61 bp):
AAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACCCTTGAGACAGTTTTCCTTTG
Found at i:9193 original size:29 final size:29
Alignment explanation
Indices: 9135--9213 Score: 117
Period size: 28 Copynumber: 2.8 Consensus size: 29
9125 TTAAAAACCC
9135 TTGAGACAGTTTTCCTTTGAAACAAGTTT
1 TTGAGACAGTTTTCCTTTGAAACAAGTTT
9164 TTGAGACAG-TTT-CTCTTGAAACAAGTTT
1 TTGAGACAGTTTTCCT-TTGAAACAAGTTT
* *
9192 TTGAGACAATTTTCCTTCGAAA
1 TTGAGACAGTTTTCCTTTGAAA
9214 TAAAATTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
27 2 0.04
28 24 0.53
29 17 0.38
30 2 0.04
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.39
Consensus pattern (29 bp):
TTGAGACAGTTTTCCTTTGAAACAAGTTT
Found at i:9200 original size:13 final size:13
Alignment explanation
Indices: 9150--9204 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
9140 ACAGTTTTCC
9150 TTTGAAACAAGTT
1 TTTGAAACAAGTT
*
9163 TTTGAGAC-AGTTT
1 TTTGAAACAAG-TT
9176 CTCTTGAAACAAGTT
1 -T-TTGAAACAAGTT
*
9191 TTTGAGACAA-TT
1 TTTGAAACAAGTT
9203 TT
1 TT
9205 CCTTCGAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
12 6 0.17
13 17 0.49
14 2 0.06
15 8 0.23
16 2 0.06
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (13 bp):
TTTGAAACAAGTT
Found at i:10028 original size:136 final size:136
Alignment explanation
Indices: 9779--10364 Score: 872
Period size: 136 Copynumber: 4.3 Consensus size: 136
9769 TTTCCAATGG
* * *
9779 AGAGTGGAGAAGAAATTCATAATGAGAAGAACTTGTTCGACCTATCACTCAATTCATGACATTTC
1 AGAG-GGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTC
*
9844 GAATCAGTGACACCTCGCTTGAGGGATTGACATTTTCAATTGAGAGTTCATAATGAGAAGAACTC
65 GAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTC
9909 ATCCGAC
130 ATCCGAC
* * * **
9916 AGAGGGAGAAGAAGTTCCTAATGAGAATAACTTGTTCGACATATCACTCGATTCACGGTATTTCG
1 AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCG
9981 AATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCA
66 AATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCA
10046 TCCGAC
131 TCCGAC
* * * *
10052 AGAGGGAGAAGAAGTTCATAATGAGAAGAGCTTGTTCTACCTATCACTCGATTCAC-AGTATTTT
1 AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGA-CATTTC
* * *
10116 GAATTAGTGACGCCTCGCTTGAGGGATTAACATTTCCAA-TGAAGAGTTCATAATGAGAAGAACT
65 GAATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTG-AGAGTTCATAATGAGAAGAACT
10180 CATCCGAC
129 CATCCGAC
** *
10188 AGAGGGAGAAGAAGTTCATAATGAGAAGGGCTTGTTCGACCTATCACTCGATTCACGACATTTTG
1 AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCG
** * * * * *
10253 AATCAGTGATGCCTTGCTTGAGGGATTGACATTTCTAATGGAGAGTTCATAATGAAAAGAATTCA
66 AATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCA
*
10318 TCCAAC
131 TCCGAC
*
10324 A-AGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCT
1 AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCT
10365 CAGATCAACA
Statistics
Matches: 411, Mismatches: 34, Indels: 10
0.90 0.07 0.02
Matches are distributed among these distances:
135 39 0.09
136 366 0.89
137 6 0.01
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.27
Consensus pattern (136 bp):
AGAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTCGACCTATCACTCGATTCACGACATTTCG
AATCAGTGACACCTCGCTTGAGGGATTGACATTTCCAATTGAGAGTTCATAATGAGAAGAACTCA
TCCGAC
Found at i:15997 original size:22 final size:23
Alignment explanation
Indices: 15972--16017 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
15962 TTACAATTCC
15972 TTAATCTT-TTAT-TTATCTTGTT
1 TTAATCTTATT-TCTTATCTTGTT
15994 TTAATCTTATTTCTTATCTTGTT
1 TTAATCTTATTTCTTATCTTGTT
16017 T
1 T
16018 CCAGCACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.67
Consensus pattern (23 bp):
TTAATCTTATTTCTTATCTTGTT
Found at i:28275 original size:22 final size:23
Alignment explanation
Indices: 28250--28295 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
28240 TTGCAATTCC
28250 TTAATC-T-TTTCTTTATCTTGTT
1 TTAATCTTATTTC-TTATCTTGTT
28272 TTAATCTTATTTCTTATCTTGTT
1 TTAATCTTATTTCTTATCTTGTT
28295 T
1 T
28296 CCAGCACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.27
23 12 0.55
24 4 0.18
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.67
Consensus pattern (23 bp):
TTAATCTTATTTCTTATCTTGTT
Found at i:29106 original size:11 final size:12
Alignment explanation
Indices: 29090--29119 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
29080 GTAAGTATGT
29090 ATTTATTTC-TA
1 ATTTATTTCTTA
29101 ATTTATTTCTTA
1 ATTTATTTCTTA
29113 ATTTATT
1 ATTTATT
29120 CATGCAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 9 0.50
12 9 0.50
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTATTTCTTA
Found at i:30218 original size:13 final size:13
Alignment explanation
Indices: 30185--30250 Score: 69
Period size: 13 Copynumber: 4.9 Consensus size: 13
30175 ATTCAACCCG
30185 TTGACTTTGACACA
1 TTGACTTTGAC-CA
*
30199 TTTACTTTGACCA
1 TTGACTTTGACCA
*
30212 TTGACTTTGACCG
1 TTGACTTTGACCA
* * *
30225 TTAACTTTAACCTG
1 TTGACTTTGACC-A
30239 TTGACTTTGACC
1 TTGACTTTGACC
30251 GAAAAGTCAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
13 23 0.52
14 21 0.48
ACGTcount: A:0.23, C:0.23, G:0.14, T:0.41
Consensus pattern (13 bp):
TTGACTTTGACCA
Found at i:30242 original size:27 final size:26
Alignment explanation
Indices: 30182--30251 Score: 86
Period size: 27 Copynumber: 2.6 Consensus size: 26
30172 CTAATTCAAC
* * *
30182 CCGTTGACTTTGACACATTTACTTTGA
1 CCGTTGACTTTGAC-CGTTAACTTTAA
*
30209 CCATTGACTTTGACCGTTAACTTTAA
1 CCGTTGACTTTGACCGTTAACTTTAA
30235 CCTGTTGACTTTGACCG
1 CC-GTTGACTTTGACCG
30252 AAAAGTCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 11 0.30
27 26 0.70
ACGTcount: A:0.21, C:0.24, G:0.16, T:0.39
Consensus pattern (26 bp):
CCGTTGACTTTGACCGTTAACTTTAA
Found at i:35100 original size:2 final size:2
Alignment explanation
Indices: 35093--35131 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
35083 ACAAGCAATA
*
35093 AT AT AT AT AT AT AT AA 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 AT AT AT AT AT AT A
35132 AAATCATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:36813 original size:3 final size:3
Alignment explanation
Indices: 36805--36850 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
36795 TTTAGTTTCA
*
36805 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT T-T TTT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36851 CTCTATTTGT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:37084 original size:25 final size:25
Alignment explanation
Indices: 37050--37101 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
37040 AGCCTTGCAC
37050 GCCGCCACTGGAGCCAATCAGATCT
1 GCCGCCACTGGAGCCAATCAGATCT
*
37075 GCCGCTACTGGAGCCAATCAGATCT
1 GCCGCCACTGGAGCCAATCAGATCT
37100 GC
1 GC
37102 TGCCCCCGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.23, C:0.35, G:0.25, T:0.17
Consensus pattern (25 bp):
GCCGCCACTGGAGCCAATCAGATCT
Found at i:37553 original size:20 final size:21
Alignment explanation
Indices: 37507--37554 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
37497 TAGGGGCCTA
*
37507 GGGTTGTAGATCTAGACGAAT
1 GGGTTGTAGATCTAGACGAAG
37528 GGGTTGTAGATCTAGACG-AG
1 GGGTTGTAGATCTAGACGAAG
37548 GGGTTGT
1 GGGTTGT
37555 TTTGGGGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.23, C:0.08, G:0.40, T:0.29
Consensus pattern (21 bp):
GGGTTGTAGATCTAGACGAAG
Found at i:39734 original size:3 final size:3
Alignment explanation
Indices: 39721--39770 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
39711 TAAAAAATAC
*
39721 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39768 AAT
1 AAT
39771 TGAATCAAGA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40628 original size:193 final size:198
Alignment explanation
Indices: 40292--40675 Score: 690
Period size: 193 Copynumber: 2.0 Consensus size: 198
40282 CGATAACAGG
*
40292 CATTGATACATGATCATATTATAGTAACAAACATGAATGAACGTAAGATTTTATGTTAAGAAGAT
1 CATTGATACATGATCATATTATAGTAACAAACATGAATGAACGTAAGATTTTATATT-AGAAGAT
40357 GAACTTCTAAATTTAGAAAAGGACGAACTTATAAAATTTATAGGGCGAAAACATATTTTCAATAG
65 GAACTTCT-AATTTAGAAAAGGACGAACTTATAAAATTTATAGGGCGAAAACATATTTTCAATAG
40422 AAAATATACAATAAACAAATATATTTTTAGTAAAAATATATCATCAAGCTTCCCACATATAGATA
129 AAAATATACAATAAACAAATATATTTTTAGTAAAAATATATCATCAAGCTTCCCACATATAGATA
40487 AGAAA
194 AGAAA
40492 CATTGATACATGATCATATTATA-TAACAAACATGAATGAACGTAAGATTTTATCATT-GAAGAT
1 CATTGATACATGATCATATTATAGTAACAAACATGAATGAACGTAAGATTTTAT-ATTAGAAGAT
40555 -AA-TT-T-ATTTAGAAAAGGACGAACTTATAAAATTTATAGGGCGAAAACATATTTTCAATAGA
65 GAACTTCTAATTTAGAAAAGGACGAACTTATAAAATTTATAGGGCGAAAACATATTTTCAATAGA
40616 AAATATACAATAAACAAATATATTTTTAGTAAAAATATATCATCAAGCTTCCCACATATA
130 AAATATACAATAAACAAATATATTTTTAGTAAAAATATATCATCAAGCTTCCCACATATA
40676 AATGAATTAA
Statistics
Matches: 182, Mismatches: 1, Indels: 9
0.95 0.01 0.05
Matches are distributed among these distances:
193 116 0.64
195 1 0.01
196 2 0.01
197 2 0.01
198 6 0.03
199 30 0.16
200 25 0.14
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (198 bp):
CATTGATACATGATCATATTATAGTAACAAACATGAATGAACGTAAGATTTTATATTAGAAGATG
AACTTCTAATTTAGAAAAGGACGAACTTATAAAATTTATAGGGCGAAAACATATTTTCAATAGAA
AATATACAATAAACAAATATATTTTTAGTAAAAATATATCATCAAGCTTCCCACATATAGATAAG
AAA
Found at i:40892 original size:21 final size:23
Alignment explanation
Indices: 40852--40893 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
40842 TTATATTGAA
40852 TTTAACAATAAAAATTATACAGT
1 TTTAACAATAAAAATTATACAGT
*
40875 TTTAA-AATAATAA-TATACA
1 TTTAACAATAAAAATTATACA
40894 TAAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 6 0.33
22 7 0.39
23 5 0.28
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (23 bp):
TTTAACAATAAAAATTATACAGT
Found at i:41257 original size:17 final size:17
Alignment explanation
Indices: 41235--41268 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
41225 TTGAAATTCC
41235 TCATACTCAATATTATA
1 TCATACTCAATATTATA
41252 TCATACTCAATATTATA
1 TCATACTCAATATTATA
41269 AACAATGAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (17 bp):
TCATACTCAATATTATA
Found at i:42414 original size:165 final size:168
Alignment explanation
Indices: 42160--42537 Score: 424
Period size: 165 Copynumber: 2.3 Consensus size: 168
42150 TAAAATAAAT
* * * *
42160 TTAAAAAGGTCTGTTTGAGATATGGGTCAATACTAGATCAATCATATTTGGGCTCAACATACTTC
1 TTAAAAATGTCTATTCGAGATATGGGTCAATACTAGATCAATCATATTTGGGCTCAACATACTTA
* ** * * *
42225 TGAGCTTATAGGGAATACTTAATAAATTTATTCAATCAATAAATC-ATGTCATGAGTCAAAATTG
66 TGAGCTCATAAAGAATAATTAATAAATTGATTCAATCAACAAATCGA-GTCATGAGTCAAAATTG
** * *
42289 GGTAAGGCCAACCTTAGTCAAAGTCAATT-G-ATAA-AG
130 AATAAGGCCAACCTTAGTCAAAATCAATTAGTAAAACAG
* * * * *
42325 TTAAATATGTCTATTCGAGATATGGGTCAATACTAGGT-ATATCCTATTTGGGCTCGATATACTT
1 TTAAAAATGTCTATTCGAGATATGGGTCAATACTAGATCA-ATCATATTTGGGCTCAACATACTT
* * * * *
42389 ATGAGCTCATAAAGAATAATTAATAAGTTGGTTTAGTCAACAAATCGAGTCATGATTCAAAATTG
65 ATGAGCTCATAAAGAATAATTAATAAATTGATTCAATCAACAAATCGAGTCATGAGTCAAAATTG
* * *
42454 AATAATGTCAACCTTAGTCAAAATCGATTAGTAAAATCGAG
130 AATAAGGCCAACCTTAGTCAAAATCAATTAGTAAAA-C-AG
* *
42495 TTAAAAATGTCTATTCGAGATATGGGTTAGTACTAGATCAATC
1 TTAAAAATGTCTATTCGAGATATGGGTCAATACTAGATCAATC
42538 CTAGTTAGGC
Statistics
Matches: 174, Mismatches: 31, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
164 1 0.01
165 128 0.74
166 2 0.01
167 3 0.02
170 39 0.22
171 1 0.01
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (168 bp):
TTAAAAATGTCTATTCGAGATATGGGTCAATACTAGATCAATCATATTTGGGCTCAACATACTTA
TGAGCTCATAAAGAATAATTAATAAATTGATTCAATCAACAAATCGAGTCATGAGTCAAAATTGA
ATAAGGCCAACCTTAGTCAAAATCAATTAGTAAAACAG
Found at i:59418 original size:22 final size:22
Alignment explanation
Indices: 59393--59438 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
59383 ATTGGTTATT
*
59393 ATATATATGATTTTTATCATGA
1 ATATATATGATGTTTATCATGA
*
59415 ATATATATGATGTTTATTATGA
1 ATATATATGATGTTTATCATGA
59437 AT
1 AT
59439 GTTACTTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (22 bp):
ATATATATGATGTTTATCATGA
Found at i:59671 original size:65 final size:61
Alignment explanation
Indices: 59588--59709 Score: 147
Period size: 61 Copynumber: 1.9 Consensus size: 61
59578 GCAAGTTTAT
* *
59588 ATTAGCACTAGTGTGTAAAGACAGTAAGTGCAGGTGGAGGGCACAACCTTATGTGTCATATCCAG
1 ATTAGCACTAGTGTGT-AA-AC-CT-AGTGCAGGTGGAGGGCACAACCTTATGCGTCATATCCAG
* * *
59653 ATTAGCACTAGAT-TGTAAACCTAGTGTAGGTGGTGGGCACGACCTTATGCGTCATAT
1 ATTAGCACTAG-TGTGTAAACCTAGTGCAGGTGGAGGGCACAACCTTATGCGTCATAT
59710 TGGGATTAAC
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
61 31 0.61
62 1 0.02
63 2 0.04
64 2 0.04
65 14 0.27
66 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (61 bp):
ATTAGCACTAGTGTGTAAACCTAGTGCAGGTGGAGGGCACAACCTTATGCGTCATATCCAG
Found at i:64486 original size:24 final size:24
Alignment explanation
Indices: 64451--64514 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 24
64441 ATCTGTTTTC
64451 GGATT-TGATTCTGATACCTGACCT
1 GGATTCTG-TTCTGATACCTGACCT
** *
64475 GGATTCTGTTCTGATTTCTGATCT
1 GGATTCTGTTCTGATACCTGACCT
*
64499 GGATTCTGTTATGATA
1 GGATTCTGTTCTGATA
64515 TATAATCTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 32 0.94
25 2 0.06
ACGTcount: A:0.19, C:0.16, G:0.22, T:0.44
Consensus pattern (24 bp):
GGATTCTGTTCTGATACCTGACCT
Found at i:64522 original size:24 final size:24
Alignment explanation
Indices: 64473--64530 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
64463 GATACCTGAC
* * * *
64473 CTGGATTCTGTTCTGATTTCTGAT
1 CTGGATTCTGTTATGATATATAAT
64497 CTGGATTCTGTTATGATATATAAT
1 CTGGATTCTGTTATGATATATAAT
*
64521 CTGAATTCTG
1 CTGGATTCTG
64531 ATTTGATTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.21, C:0.14, G:0.19, T:0.47
Consensus pattern (24 bp):
CTGGATTCTGTTATGATATATAAT
Found at i:70955 original size:20 final size:20
Alignment explanation
Indices: 70926--70968 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
70916 TTTCCACCAC
70926 ATGCAACTATAT-GCTCCTAA
1 ATGCAACTATATGGCT-CTAA
*
70946 ATGCATCTATATGGCTCTAA
1 ATGCAACTATATGGCTCTAA
70966 ATG
1 ATG
70969 AGCCAGACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGGCTCTAA
Found at i:73791 original size:20 final size:20
Alignment explanation
Indices: 73762--73804 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
73752 ATTTCACCAC
73762 ATGCAACTATATGATCCTAA
1 ATGCAACTATATGATCCTAA
* *
73782 ATGCATCTATATGGTCCTAA
1 ATGCAACTATATGATCCTAA
73802 ATG
1 ATG
73805 ACCTCTTAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.14, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:78417 original size:49 final size:46
Alignment explanation
Indices: 78306--78427 Score: 138
Period size: 49 Copynumber: 2.6 Consensus size: 46
78296 GTAACCATGC
*
78306 AAATAAGCTTATGAGCTTACGGAATAATGGCAAGTATATTGAAAAA
1 AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
* * * **
78352 AAATAAGCTTACGAGCTTATGGAATTTTAAATGGTAAGTATTTTG-GTAA
1 AAATAAGCTTATGAGCTTATGGAA---T-AATGGCAAGTATATTGAAAAA
*
78401 AAATAAGCTTATGAGCTTATGGGATAA
1 AAATAAGCTTATGAGCTTATGGAATAA
78428 AAGGTAAGAA
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
45 2 0.03
46 23 0.36
49 25 0.39
50 14 0.22
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.31
Consensus pattern (46 bp):
AAATAAGCTTATGAGCTTATGGAATAATGGCAAGTATATTGAAAAA
Found at i:87381 original size:22 final size:22
Alignment explanation
Indices: 87356--87401 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
87346 ACTGGTTATT
87356 ATATATATGATATTTATCATGA
1 ATATATATGATATTTATCATGA
* * * *
87378 ATATATGTTATGTTTATTATGA
1 ATATATATGATATTTATCATGA
87400 AT
1 AT
87402 GCTACTTTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (22 bp):
ATATATATGATATTTATCATGA
Found at i:95331 original size:21 final size:22
Alignment explanation
Indices: 95307--95368 Score: 65
Period size: 21 Copynumber: 2.8 Consensus size: 22
95297 CCTCCCAAAT
95307 TTTAACTTTTCTTTCTCTTTC-
1 TTTAACTTTTCTTTCTCTTTCA
* *
95328 TTTATTCATTT-TTTCTCTTTCA
1 TTTA-ACTTTTCTTTCTCTTTCA
95350 TGTTAACTTTTACTTTCTC
1 T-TTAACTTTT-CTTTCTC
95369 CTCTCTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
21 14 0.44
22 9 0.28
23 3 0.09
24 6 0.19
ACGTcount: A:0.13, C:0.21, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTAACTTTTCTTTCTCTTTCA
Found at i:102831 original size:30 final size:30
Alignment explanation
Indices: 102795--102866 Score: 144
Period size: 30 Copynumber: 2.4 Consensus size: 30
102785 CAATATTTTT
102795 TTCTAAATCATTGATTTTGACTTCTGAAAG
1 TTCTAAATCATTGATTTTGACTTCTGAAAG
102825 TTCTAAATCATTGATTTTGACTTCTGAAAG
1 TTCTAAATCATTGATTTTGACTTCTGAAAG
102855 TTCTAAATCATT
1 TTCTAAATCATT
102867 TTTCAAAATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (30 bp):
TTCTAAATCATTGATTTTGACTTCTGAAAG
Found at i:104342 original size:19 final size:20
Alignment explanation
Indices: 104281--104350 Score: 90
Period size: 20 Copynumber: 3.5 Consensus size: 20
104271 TATTGTTCAT
* *
104281 TACTGTTCACACAATATC-G
1 TACTATTCATACAATATCAG
104300 ATACTATTCATACAATATCAG
1 -TACTATTCATACAATATCAG
*
104321 TACTATTCATACATTA-CAG
1 TACTATTCATACAATATCAG
104340 TACTATTCATA
1 TACTATTCATA
104351 AAAAAATTAT
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 14 0.30
20 31 0.67
21 1 0.02
ACGTcount: A:0.37, C:0.21, G:0.06, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAATATCAG
Found at i:112923 original size:14 final size:14
Alignment explanation
Indices: 112904--112932 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
112894 ACGGTCAACG
112904 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
112918 GTCGGGTCGGGTCA
1 GTCGGGTCGGGTCA
112932 G
1 G
112933 ACCGGTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.07, C:0.21, G:0.52, T:0.21
Consensus pattern (14 bp):
GTCGGGTCGGGTCA
Found at i:119392 original size:7 final size:7
Alignment explanation
Indices: 119380--119424 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
119370 GTCAAAGGAA
119380 GTCAACG
1 GTCAACG
119387 GTCAACG
1 GTCAACG
*
119394 GTC-ATG
1 GTCAACG
119400 GTCAACG
1 GTCAACG
*
119407 ATCAACG
1 GTCAACG
119414 GTCAACG
1 GTCAACG
119421 GTCA
1 GTCA
119425 GGTCGGGTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:119405 original size:20 final size:20
Alignment explanation
Indices: 119380--119417 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
119370 GTCAAAGGAA
*
119380 GTCAACGGTCAACGGTCATG
1 GTCAACGATCAACGGTCATG
119400 GTCAACGATCAACGGTCA
1 GTCAACGATCAACGGTCA
119418 ACGGTCAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.18
Consensus pattern (20 bp):
GTCAACGATCAACGGTCATG
Found at i:119474 original size:19 final size:20
Alignment explanation
Indices: 119452--119494 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
119442 TCAGTCAGGT
* *
119452 CGGTTCGGACCGGT-TAAAC
1 CGGTTCGAACCGGTCGAAAC
119471 CGGTTCGAACCGGTCGAAAC
1 CGGTTCGAACCGGTCGAAAC
119491 CGGT
1 CGGT
119495 CAGAACAGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.62
20 8 0.38
ACGTcount: A:0.21, C:0.28, G:0.33, T:0.19
Consensus pattern (20 bp):
CGGTTCGAACCGGTCGAAAC
Found at i:119509 original size:20 final size:20
Alignment explanation
Indices: 119452--119509 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 20
119442 TCAGTCAGGT
* *
119452 CGGTTCGGACCGGTT-AAAC
1 CGGTTCGAACAGGTTGAAAC
* *
119471 CGGTTCGAACCGGTCGAAAC
1 CGGTTCGAACAGGTTGAAAC
119491 CGG-TCAGAACAGGTTGAAA
1 CGGTTC-GAACAGGTTGAAA
119510 ATCGGTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 15 0.45
20 18 0.55
ACGTcount: A:0.28, C:0.24, G:0.31, T:0.17
Consensus pattern (20 bp):
CGGTTCGAACAGGTTGAAAC
Found at i:121376 original size:23 final size:21
Alignment explanation
Indices: 121357--121438 Score: 60
Period size: 21 Copynumber: 3.9 Consensus size: 21
121347 ATGCATCCTT
121357 TGAATATGCATCGATACATCA
1 TGAATATGCATCGATACATCA
** * *
121378 TGAAGGTGCATCGATGCATTCCT
1 TGAATATGCATCGATACA-T-CA
* *
121401 TGAATGTGTATCGATACA-CTA
1 TGAATATGCATCGATACATC-A
*
121422 TGCA-ATGCATCGATACA
1 TGAATATGCATCGATACA
121439 CTCGTTGGGT
Statistics
Matches: 47, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
20 12 0.26
21 18 0.38
22 1 0.02
23 16 0.34
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.29
Consensus pattern (21 bp):
TGAATATGCATCGATACATCA
Found at i:125237 original size:20 final size:20
Alignment explanation
Indices: 125212--125275 Score: 92
Period size: 20 Copynumber: 3.2 Consensus size: 20
125202 GATGTTTTTG
* *
125212 AGTATCGATACTGTTCACAC
1 AGTATCGATACTATTCATAC
*
125232 AGTATCGATACTATTTATAC
1 AGTATCGATACTATTCATAC
*
125252 AATATCGATACTATTCATAC
1 AGTATCGATACTATTCATAC
125272 AGTA
1 AGTA
125276 CATTACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (20 bp):
AGTATCGATACTATTCATAC
Found at i:125743 original size:51 final size:52
Alignment explanation
Indices: 125639--125749 Score: 154
Period size: 51 Copynumber: 2.1 Consensus size: 52
125629 ACAAAACCAA
* * *
125639 AAACCATATTTAGTATACTTGTTATAGATAGAGTAAAACTTTTATCACCATCT
1 AAACCATATTTAGTATACTAGTTATAGA-ACAGTAAAAATTTTATCACCATCT
*
125692 AAACCATATTTAGTATACTAGTTGTAG-ACAGTAAAAATTTTA-CAGCCATCT
1 AAACCATATTTAGTATACTAGTTATAGAACAGTAAAAATTTTATCA-CCATCT
125743 AAACCAT
1 AAACCAT
125750 TATCTTTCTC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
50 2 0.04
51 26 0.49
53 25 0.47
ACGTcount: A:0.40, C:0.16, G:0.10, T:0.34
Consensus pattern (52 bp):
AAACCATATTTAGTATACTAGTTATAGAACAGTAAAAATTTTATCACCATCT
Found at i:126061 original size:17 final size:17
Alignment explanation
Indices: 126039--126071 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
126029 TTCAATTTCA
126039 AATCAAAACTGAAATAT
1 AATCAAAACTGAAATAT
126056 AATCAAAACTGAAATA
1 AATCAAAACTGAAATA
126072 AGTCAGCGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.21
Consensus pattern (17 bp):
AATCAAAACTGAAATAT
Found at i:132215 original size:23 final size:22
Alignment explanation
Indices: 132151--132215 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 22
132141 TCTTTTTCTC
*
132151 TCTTTTTTCTTCTTGTTCGAACA
1 TCTTTTTTCTT-TTTTTCGAACA
132174 TCTTTTTTTCTTTTCTTTCGAACTA
1 TC-TTTTTTCTTTT-TTTCGAAC-A
132199 T-TTTTTTCCTTTTTTTC
1 TCTTTTTT-CTTTTTTTC
132216 CAATGGATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 14 0.38
24 21 0.57
25 2 0.05
ACGTcount: A:0.09, C:0.20, G:0.05, T:0.66
Consensus pattern (22 bp):
TCTTTTTTCTTTTTTTCGAACA
Found at i:144502 original size:2 final size:2
Alignment explanation
Indices: 144495--144519 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
144485 CTTTAAATTG
144495 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 A
144520 ATTCGGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:146975 original size:29 final size:29
Alignment explanation
Indices: 146933--147014 Score: 146
Period size: 29 Copynumber: 2.8 Consensus size: 29
146923 AAACTAAATT
146933 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
146962 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
146991 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
147015 GTTAGGTGAG
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
29 46 0.90
30 5 0.10
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:157157 original size:12 final size:12
Alignment explanation
Indices: 157140--157194 Score: 67
Period size: 12 Copynumber: 4.7 Consensus size: 12
157130 TATTTTTTTT
*
157140 CAAAAAAAAAAA
1 CAAAAAAAAAAG
*
157152 C-AAAAAAAAGG
1 CAAAAAAAAAAG
*
157163 CAAAAAAAAAGG
1 CAAAAAAAAAAG
*
157175 CACAAAAAAAAG
1 CAAAAAAAAAAG
157187 CAAAAAAA
1 CAAAAAAA
157195 GCCAAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 9 0.24
12 28 0.76
ACGTcount: A:0.80, C:0.11, G:0.09, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAAG
Found at i:168049 original size:11 final size:11
Alignment explanation
Indices: 168033--168087 Score: 58
Period size: 12 Copynumber: 4.7 Consensus size: 11
168023 AAATTTTGGC
168033 TTTTTTTGCTTT
1 TTTTTTTGC-TT
168045 TTTTTTGTGCCTT
1 TTTTTT-TG-CTT
*
168058 TTTTTTGTGCCT
1 TTTTTT-TGCTT
168070 TTTTTTTG-TT
1 TTTTTTTGCTT
168080 TTTTTTTG
1 TTTTTTTG
168088 AAAAAAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 9 0.23
11 2 0.05
12 14 0.36
13 13 0.33
14 1 0.03
ACGTcount: A:0.00, C:0.09, G:0.13, T:0.78
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:168059 original size:13 final size:13
Alignment explanation
Indices: 168033--168078 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
168023 AAATTTTGGC
*
168033 TTTTTT-TGCTTT
1 TTTTTTGTGCCTT
168045 TTTTTTGTGCCTT
1 TTTTTTGTGCCTT
168058 TTTTTTGTGCCTT
1 TTTTTTGTGCCTT
168071 TTTTTTGT
1 TTTTTTGT
168079 TTTTTTTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 6 0.19
13 26 0.81
ACGTcount: A:0.00, C:0.11, G:0.13, T:0.76
Consensus pattern (13 bp):
TTTTTTGTGCCTT
Found at i:184339 original size:13 final size:12
Alignment explanation
Indices: 184315--184357 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
184305 AAATTTTGGC
184315 TTTTTT-TGCTT
1 TTTTTTGTGCTT
184326 TTTTTTGTGCCTT
1 TTTTTTGTG-CTT
**
184339 TTTTTTGTTTTT
1 TTTTTTGTGCTT
184351 TTTTTTG
1 TTTTTTG
184358 AAAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 6 0.21
12 11 0.39
13 11 0.39
ACGTcount: A:0.00, C:0.07, G:0.12, T:0.81
Consensus pattern (12 bp):
TTTTTTGTGCTT
Found at i:200716 original size:85 final size:84
Alignment explanation
Indices: 200627--200782 Score: 181
Period size: 85 Copynumber: 1.8 Consensus size: 84
200617 ATATATATAT
* * * * *
200627 ATATATATATGGCATATAA-TCACGACACACGAATGTGTGTCATCTT-TTCTAATGACGTGTGCT
1 ATATATACATGGCATA-AATTCACGACACACAAAAGTGTGTCATCTTATT-T-ATGACGGGGGCT
200690 TCAATGACATGCAATGTAAGTC
63 TCAATGACATGCAATGTAAGTC
* * * *
200712 ATATATGCATGTCATAAATTTATGACACACAAAAGTGTGTCATCTTCATTTATGACGGGGGCTTC
1 ATATATACATGGCATAAATTCACGACACACAAAAGTGTGTCATCTT-ATTTATGACGGGGGCTTC
200777 AATGAC
65 AATGAC
200783 GCTCATTGAG
Statistics
Matches: 59, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
84 2 0.03
85 54 0.92
86 1 0.02
87 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (84 bp):
ATATATACATGGCATAAATTCACGACACACAAAAGTGTGTCATCTTATTTATGACGGGGGCTTCA
ATGACATGCAATGTAAGTC
Found at i:200810 original size:13 final size:13
Alignment explanation
Indices: 200789--200842 Score: 81
Period size: 13 Copynumber: 4.2 Consensus size: 13
200779 TGACGCTCAT
*
200789 TGAGCGTCATAAA
1 TGAGTGTCATAAA
200802 TGAGTGTCATAAA
1 TGAGTGTCATAAA
* *
200815 TGTGAGTCATAAA
1 TGAGTGTCATAAA
200828 TGAGTGTCATAAA
1 TGAGTGTCATAAA
200841 TG
1 TG
200843 CGCGACATAG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (13 bp):
TGAGTGTCATAAA
Found at i:200851 original size:26 final size:26
Alignment explanation
Indices: 200796--200851 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
200786 CATTGAGCGT
* *
200796 CATAAATGAGTGTCATAAATGTGAGT
1 CATAAATGAGTGTCATAAATGCGAGA
*
200822 CATAAATGAGTGTCATAAATGCGCGA
1 CATAAATGAGTGTCATAAATGCGAGA
200848 CATA
1 CATA
200852 GATTTATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.27
Consensus pattern (26 bp):
CATAAATGAGTGTCATAAATGCGAGA
Found at i:202266 original size:2 final size:2
Alignment explanation
Indices: 202259--202284 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
202249 TAATGAACAA
202259 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
202285 GATTGATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:207125 original size:85 final size:83
Alignment explanation
Indices: 206977--207157 Score: 213
Period size: 85 Copynumber: 2.2 Consensus size: 83
206967 CACGACACAC
* * * *
206977 AAATGTGTGTCATCTTTTTTAATGGCGAGTGCTTCAATGACACGCAATGTAAGTCATACATGCGT
1 AAATGTGTGTCATCTTATTTAATGACGAGGGCTTCAATGACACGCAATGTAAGTCATAAATGCGT
*
207042 GTCATAAATTTATGATACAT
66 GTCATAAATGTATG-T-CAT
* * * * *
207062 AAATGTGTGTCATCTTAATTT-ATGACGGGGGTTTCAATGACGCTCAATG-ATCGTCATAAATGC
1 AAATGTGTGTCATCTT-ATTTAATGACGAGGGCTTCAATGACACGCAATGTA-AGTCATAAATGC
*
207125 GTGTCATAAATGTGTGTCAT
64 GTGTCATAAATGTATGTCAT
207145 AAATGTGTGTCAT
1 AAATGTGTGTCAT
207158 AAATGCGCGT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
83 16 0.19
84 2 0.02
85 62 0.75
86 3 0.04
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (83 bp):
AAATGTGTGTCATCTTATTTAATGACGAGGGCTTCAATGACACGCAATGTAAGTCATAAATGCGT
GTCATAAATGTATGTCAT
Found at i:207130 original size:13 final size:13
Alignment explanation
Indices: 207114--207169 Score: 85
Period size: 13 Copynumber: 4.3 Consensus size: 13
207104 CTCAATGATC
207114 GTCATAAATGCGT
1 GTCATAAATGCGT
*
207127 GTCATAAATGTGT
1 GTCATAAATGCGT
*
207140 GTCATAAATGTGT
1 GTCATAAATGCGT
*
207153 GTCATAAATGCGC
1 GTCATAAATGCGT
207166 GTCA
1 GTCA
207170 AATTTATGAC
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 40 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.32
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:208196 original size:85 final size:83
Alignment explanation
Indices: 208048--208228 Score: 213
Period size: 85 Copynumber: 2.2 Consensus size: 83
208038 CACGACACAC
* * * *
208048 AAATGTGTGTCATCTTTTTTAATGGCGAGTGCTTCAATGACACGCAATGTAAGTCATACATGCGT
1 AAATGTGTGTCATCTTATTTAATGACGAGGGCTTCAATGACACGCAATGTAAGTCATAAATGCGT
*
208113 GTCATAAATTTATGATACAT
66 GTCATAAATGTATG-T-CAT
* * * * *
208133 AAATGTGTGTCATCTTAATTT-ATGACGGGGGTTTCAATGACGCTCAATG-ATCGTCATAAATGC
1 AAATGTGTGTCATCTT-ATTTAATGACGAGGGCTTCAATGACACGCAATGTA-AGTCATAAATGC
*
208196 GTGTCATAAATGTGTGTCAT
64 GTGTCATAAATGTATGTCAT
208216 AAATGTGTGTCAT
1 AAATGTGTGTCAT
208229 AAATGCGCGT
Statistics
Matches: 83, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
83 16 0.19
84 2 0.02
85 62 0.75
86 3 0.04
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.35
Consensus pattern (83 bp):
AAATGTGTGTCATCTTATTTAATGACGAGGGCTTCAATGACACGCAATGTAAGTCATAAATGCGT
GTCATAAATGTATGTCAT
Found at i:208201 original size:13 final size:13
Alignment explanation
Indices: 208185--208245 Score: 95
Period size: 13 Copynumber: 4.7 Consensus size: 13
208175 CTCAATGATC
208185 GTCATAAATGCGT
1 GTCATAAATGCGT
*
208198 GTCATAAATGTGT
1 GTCATAAATGCGT
*
208211 GTCATAAATGTGT
1 GTCATAAATGCGT
*
208224 GTCATAAATGCGC
1 GTCATAAATGCGT
208237 GTCATAAAT
1 GTCATAAAT
208246 TTATGACGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (13 bp):
GTCATAAATGCGT
Found at i:208207 original size:26 final size:25
Alignment explanation
Indices: 208178--208245 Score: 82
Period size: 26 Copynumber: 2.6 Consensus size: 25
208168 AATGACGCTC
208178 AATGATCGTCATAAATGCGTGTCATA
1 AATG-TCGTCATAAATGCGTGTCATA
* *
208204 AATGTGTGTCATAAATGTGTGTCATA
1 AATGT-CGTCATAAATGCGTGTCATA
*
208230 AATGCGCGTCATAAAT
1 AATG-TCGTCATAAAT
208246 TTATGACGCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.03
26 35 0.97
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (25 bp):
AATGTCGTCATAAATGCGTGTCATA
Found at i:213288 original size:40 final size:40
Alignment explanation
Indices: 213224--213355 Score: 167
Period size: 40 Copynumber: 3.3 Consensus size: 40
213214 TTATTACGTA
* *
213224 CAATACATCATCATTATTGCAGTTGGGTGTGTATCCCATG
1 CAATACATCACCATTATTGTAGTTGGGTGTGTATCCCATG
* * *
213264 CAAAACATCACCATTATTGTAGTTGGGTGTGTATCCCGTA
1 CAATACATCACCATTATTGTAGTTGGGTGTGTATCCCATG
* * * *
213304 CAATACATCACCATTCTTGTATTTAGGTGTGTATCTCATAG
1 CAATACATCACCATTATTGTAGTTGGGTGTGTATCCCAT-G
213345 -AATACATCACC
1 CAATACATCACC
213356 TTAATTATTG
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
40 79 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (40 bp):
CAATACATCACCATTATTGTAGTTGGGTGTGTATCCCATG
Found at i:213733 original size:40 final size:41
Alignment explanation
Indices: 213690--213931 Score: 190
Period size: 40 Copynumber: 5.9 Consensus size: 41
213680 GTTCATATAA
*
213690 TTAGGTGTGTATCTCATACAATACATCACTATTATTATGA-
1 TTAGGTGTGTATCTCATACAATACATCACTATTATTGTGAG
* * * *
213730 TTAGGTTTGTATCACGTACAATACATCA-TCATTATTG-CAG
1 TTAGGTGTGTATCTCATACAATACATCACT-ATTATTGTGAG
* * * * * *
213770 TTGGGTGTGTATCCCGTGCAAAACATCACCATTATTGT-AG
1 TTAGGTGTGTATCTCATACAATACATCACTATTATTGTGAG
* * * * * * *
213810 TTGGGTGTGTATCCCGTACAATACATCACCACTCTTGT-AT
1 TTAGGTGTGTATCTCATACAATACATCACTATTATTGTGAG
*
213850 TTAGGTATGTATCTCATACAATACATCACCTTAATTATTGTG-G
1 TTAGGTGTGTATCTCATACAATACATCA-C-T-ATTATTGTGAG
* * * *
213893 GTAGGTGTGTATTTCCATACAATACATCACCATTCTTGT
1 TTAGGTGTGTATCT-CATACAATACATCACTATTATTGT
213932 ATTTATATGT
Statistics
Matches: 164, Mismatches: 29, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
39 2 0.01
40 122 0.74
41 8 0.05
43 18 0.11
44 14 0.09
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (41 bp):
TTAGGTGTGTATCTCATACAATACATCACTATTATTGTGAG
Found at i:213861 original size:80 final size:81
Alignment explanation
Indices: 213690--213936 Score: 230
Period size: 80 Copynumber: 3.0 Consensus size: 81
213680 GTTCATATAA
* * * * * * *
213690 TTAGGTGTGTATCTCATACAATACATCA-CTATTATTAT-GATTAGGTTTGTATCACGTACAATA
1 TTAGGTATGTATCCCATACAAAACATCACCTATTATTGTAG-GTAGGTGTGTATCCCGTACAATA
* * * *
213753 CATCATCATTATTGCAG
65 CATCACCATTCTTGTAT
* * * * * *
213770 TTGGGTGTGTATCCCGTGCAAAACATCACC-ATTATTGTAGTTGGGTGTGTATCCCGTACAATAC
1 TTAGGTATGTATCCCATACAAAACATCACCTATTATTGTAGGTAGGTGTGTATCCCGTACAATAC
*
213834 ATCACCACTCTTGTAT
66 ATCACCATTCTTGTAT
* * * * *
213850 TTAGGTATGTATCTCATACAATACATCACCTTAATTATTGTGGGTAGGTGTGTATTTCCATACAA
1 TTAGGTATGTATCCCATACAAAACATCACC-T-ATTATTGTAGGTAGGTGTGTA-TCCCGTACAA
213915 TACATCACCATTCTTGTAT
63 TACATCACCATTCTTGTAT
213934 TTA
1 TTA
213937 TATGTGTATG
Statistics
Matches: 135, Mismatches: 26, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
80 86 0.64
81 2 0.01
83 18 0.13
84 29 0.21
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.38
Consensus pattern (81 bp):
TTAGGTATGTATCCCATACAAAACATCACCTATTATTGTAGGTAGGTGTGTATCCCGTACAATAC
ATCACCATTCTTGTAT
Found at i:213962 original size:84 final size:82
Alignment explanation
Indices: 213813--213972 Score: 187
Period size: 84 Copynumber: 1.9 Consensus size: 82
213803 ATTGTAGTTG
* * *
213813 GGTGTGTATCCCGTACAATACATCACCACTCTTGTATTTAGGTATGTATCTCATACAATACATCA
1 GGTGTGTATCCCATACAATACATCACCACTCTTGTATTTA-GTATGTATATAATACAATACATCA
* *
213878 CCTTAATTATTGTGGGTA
65 CATCAATTATTGTGGGTA
* * * * *
213896 GGTGTGTATTTCCATACAATACATCACCATTCTTGTATTTA-TATGTGTATGAATTACGATATAT
1 GGTGTGTA-TCCCATACAATACATCACCACTCTTGTATTTAGTATGTATAT-AA-TACAATACAT
213960 CACATCAATTATT
63 CACATCAATTATT
213973 AGTACCAATA
Statistics
Matches: 64, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
82 7 0.11
83 9 0.14
84 48 0.75
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (82 bp):
GGTGTGTATCCCATACAATACATCACCACTCTTGTATTTAGTATGTATATAATACAATACATCAC
ATCAATTATTGTGGGTA
Found at i:214054 original size:39 final size:38
Alignment explanation
Indices: 213978--214074 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 38
213968 TTATTAGTAC
* ** *
213978 CAATACCAATTTCCTAATACATATACTCTAAAATAGTT
1 CAATACCAATATCCTGGTACATATACTCTAAATTAGTT
**
214016 CAAATACCAATATCCTGGTACATATACTCTGGATTAGTTT
1 C-AATACCAATATCCTGGTACATATACTCTAAATTAG-TT
* *
214056 CAATACCGATATCTTGGTA
1 CAATACCAATATCCTGGTA
214075 GTTATACATT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.02
39 45 0.92
40 3 0.06
ACGTcount: A:0.36, C:0.21, G:0.09, T:0.34
Consensus pattern (38 bp):
CAATACCAATATCCTGGTACATATACTCTAAATTAGTT
Found at i:218615 original size:14 final size:13
Alignment explanation
Indices: 218596--218629 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
218586 TTTTTTGTTG
218596 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
218609 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
218622 TTTGTTTT
1 TTT-TTTT
218630 TTGTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:218630 original size:8 final size:8
Alignment explanation
Indices: 218609--218648 Score: 55
Period size: 8 Copynumber: 5.0 Consensus size: 8
218599 TTTTGCCTTT
218609 TTTTTTTG
1 TTTTTTTG
*
218617 CCTTTTTTG
1 -TTTTTTTG
218626 -TTTTTTG
1 TTTTTTTG
218633 TTTTTTTG
1 TTTTTTTG
218641 TTTTTTTG
1 TTTTTTTG
218649 AAAAAAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
7 7 0.24
8 15 0.52
9 7 0.24
ACGTcount: A:0.00, C:0.05, G:0.12, T:0.82
Consensus pattern (8 bp):
TTTTTTTG
Found at i:218644 original size:13 final size:12
Alignment explanation
Indices: 218586--218647 Score: 51
Period size: 11 Copynumber: 5.2 Consensus size: 12
218576 AAATTTTGGC
*
218586 TTTTTTG-TTGT
1 TTTTTTGCTTTT
218597 TTTTTTGCCTTTT
1 TTTTTTG-CTTTT
218610 TTTTTTGCCTTTT
1 TTTTTTG-CTTTT
*
218623 TTGTTTT--TTGT
1 TT-TTTTGCTTTT
218634 TTTTTTG-TTTT
1 TTTTTTGCTTTT
218645 TTT
1 TTT
218648 GAAAAAAAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
10 4 0.09
11 18 0.41
13 18 0.41
14 4 0.09
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.82
Consensus pattern (12 bp):
TTTTTTGCTTTT
Found at i:218647 original size:16 final size:17
Alignment explanation
Indices: 218588--218648 Score: 62
Period size: 16 Copynumber: 3.9 Consensus size: 17
218578 ATTTTGGCTT
218588 TTTTGTTGTTTTTTTGCC
1 TTTT-TTGTTTTTTTGCC
218606 ---TTT-TTTTTTTGCC
1 TTTTTTGTTTTTTTGCC
*
218619 TTTTTTG-TTTTTTG-T
1 TTTTTTGTTTTTTTGCC
218634 TTTTTTGTTTTTTTG
1 TTTTTTGTTTTTTTG
218649 AAAAAAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 10 0.27
14 2 0.05
15 8 0.22
16 17 0.46
ACGTcount: A:0.00, C:0.07, G:0.13, T:0.80
Consensus pattern (17 bp):
TTTTTTGTTTTTTTGCC
Found at i:228330 original size:40 final size:39
Alignment explanation
Indices: 228268--228371 Score: 93
Period size: 40 Copynumber: 2.6 Consensus size: 39
228258 TGCAATACAT
* * *
228268 CATTATTATAATTAGGTATGTATCTCAT-ACAATAAATCAT
1 CATTATTATAGTT-GGTGTGTATCTCATCA-AATAAATCAC
* * * *
228308 GATTATTATAGTTGGATGTGTATTTTATCAAATACATCAC
1 CATTATTATAGTTGG-TGTGTATCTCATCAAATAAATCAC
*
228348 CATTATTTTAGTTGGGTGTGTATC
1 CATTATTATAGTT-GGTGTGTATC
228372 ATGTATAATA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
39 2 0.04
40 46 0.90
41 3 0.06
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (39 bp):
CATTATTATAGTTGGTGTGTATCTCATCAAATAAATCAC
Found at i:228382 original size:40 final size:40
Alignment explanation
Indices: 228338--228428 Score: 110
Period size: 40 Copynumber: 2.3 Consensus size: 40
228328 TATTTTATCA
* * * *
228338 AATACATCACCATTATTTTAGTTGGGTGTGTATCATGTAT
1 AATACATCACCACTATTGTAGTTAGGTGTGTATCATGTAC
* * *
228378 AATACATCACCACTCTTGTATTTATGTGTGTATCATGTAC
1 AATACATCACCACTATTGTAGTTAGGTGTGTATCATGTAC
*
228418 AATTCATCACC
1 AATACATCACC
228429 TTAATTATTG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (40 bp):
AATACATCACCACTATTGTAGTTAGGTGTGTATCATGTAC
Found at i:241888 original size:14 final size:16
Alignment explanation
Indices: 241855--241888 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
241845 AAACGTTTCT
241855 AATCCAATTATTGTGC
1 AATCCAATTATTGTGC
241871 AATCCAATT-TTG-GC
1 AATCCAATTATTGTGC
241885 AATC
1 AATC
241889 AATAGTAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.33
15 3 0.17
16 9 0.50
ACGTcount: A:0.32, C:0.21, G:0.12, T:0.35
Consensus pattern (16 bp):
AATCCAATTATTGTGC
Found at i:243703 original size:45 final size:45
Alignment explanation
Indices: 243636--243954 Score: 363
Period size: 45 Copynumber: 7.1 Consensus size: 45
243626 ATTCTAACAT
* * * *
243636 CTTTTCTATTGATAATGCACCCATATTCATTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATA
** * *
243681 CTTTTCTACTGATAATGTACCCATATACATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATA
** * * *
243726 CCGTTCTGTTGATAATCTATCCATATACATTTCAACTCTAGCATGA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCAT-A
* * * *
243772 -TCTTCTGTTGATAATGCACCCATATGCATTTCAACTCTAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATA
* * *
243816 CATTTCTGTTGATAATGCACCCATATGCATTTCAACTCA-AGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACT-ATAGCATA
* * * *
243861 TTTTTCTATTGATAATGTACCCATATACATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATA
* * *
243906 CTTTTCTGTTGATAATATACCCATATACATTTCAACTATGGCATC
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATA
243951 CTTT
1 CTTT
243955 CATGCCAATA
Statistics
Matches: 234, Mismatches: 36, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
44 2 0.01
45 231 0.99
46 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.09, T:0.39
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATA
Found at i:244411 original size:22 final size:20
Alignment explanation
Indices: 244373--244425 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 20
244363 TGACTCTTCA
244373 GTATCGATACCCCTACTATG
1 GTATCGATACCCCTACTATG
244393 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTATG
*
244415 GTGTCGATACC
1 GTATCGATACC
244426 TCCTTCCAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 11 0.37
22 19 0.63
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:244491 original size:20 final size:21
Alignment explanation
Indices: 244466--244521 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 21
244456 CGATGTAGCC
244466 TGGTATCGATACCCT-TACCA
1 TGGTATCGATACCCTATACCA
* *
244486 TGGTATCGATACTACTATACTA
1 TGGTATCGATAC-CCTATACCA
244508 TGGTATCGATACCC
1 TGGTATCGATACCC
244522 CCTTTGGTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.39
21 3 0.10
22 16 0.52
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (21 bp):
TGGTATCGATACCCTATACCA
Found at i:244574 original size:94 final size:95
Alignment explanation
Indices: 244373--244594 Score: 304
Period size: 94 Copynumber: 2.3 Consensus size: 95
244363 TGACTCTTCA
* * * * *
244373 GTATCGATACCCCTACTATGGTATCGATACTACCCTACTATGGTGTCGATACCTCCTTCCAGTAT
1 GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTATCGATACCCCCTTCCAGTAT
*
244438 CGATGCAAAAATTAGCTTCGATGTAGCCTG
66 CGATACAAAAATTAGCTTCGATGTAGCCTG
* **
244468 GTATCGATACCCTTACCATGGTATCGATACTACTATACTATGGTATCGATACCCCCTT-TGGTAT
1 GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTATCGATACCCCCTTCCAGTAT
* **
244532 CGATACCAAAATTAAG-TTCGATGTTTCCTG
66 CGATACAAAAATT-AGCTTCGATGTAGCCTG
*
244562 GTATCGATACCCTTACCATGGTATCAATACTAC
1 GTATCGATACCCTTACCATGGTATCGATACTAC
244595 ATCGCTTGGT
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
94 59 0.52
95 54 0.48
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (95 bp):
GTATCGATACCCTTACCATGGTATCGATACTACCATACTATGGTATCGATACCCCCTTCCAGTAT
CGATACAAAAATTAGCTTCGATGTAGCCTG
Found at i:250723 original size:45 final size:45
Alignment explanation
Indices: 250651--250977 Score: 363
Period size: 45 Copynumber: 7.3 Consensus size: 45
250641 CACTTTAAAT
* * * *
250651 TATAACAT-CTTTTTTGTTGATAATGCACCTATATGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
*
250695 TATAGTATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* * * *
250740 CATAGTATA-TCATTCTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACT-TTTCTGTTGATAATGCACCCATATACATTTCAAC
* * * *
250785 TCTAGCATGCTCTTCTGTTGATAATGCACCCATATGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* * * **
250830 TCTAGCATA-TATTTCTGTTGATAATTCACCCAAATGTATTTCAAC
1 TATAGCATACT-TTTCTGTTGATAATGCACCCATATACATTTCAAC
* * *
250875 TCTAGCATACTTTTCGGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* ** * *
250920 CATATTATACTTTTATGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
* *
250965 TATGGCATCCTTT
1 TATAGCATACTTT
250978 CATGCCAATA
Statistics
Matches: 241, Mismatches: 37, Indels: 9
0.84 0.13 0.03
Matches are distributed among these distances:
44 8 0.03
45 231 0.96
46 2 0.01
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.40
Consensus pattern (45 bp):
TATAGCATACTTTTCTGTTGATAATGCACCCATATACATTTCAAC
Found at i:251435 original size:22 final size:20
Alignment explanation
Indices: 251400--251454 Score: 92
Period size: 22 Copynumber: 2.6 Consensus size: 20
251390 TGGCTATTTA
251400 GTATCGATACCCCTACTATG
1 GTATCGATACCCCTACTATG
251420 GTATCGATACTACCCTACTATG
1 GTATCGATAC--CCCTACTATG
251442 GTATCGATACCCC
1 GTATCGATACCCC
251455 GATTTAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.39
22 20 0.61
ACGTcount: A:0.25, C:0.31, G:0.15, T:0.29
Consensus pattern (20 bp):
GTATCGATACCCCTACTATG
Found at i:251545 original size:95 final size:95
Alignment explanation
Indices: 251400--251622 Score: 270
Period size: 95 Copynumber: 2.3 Consensus size: 95
251390 TGGCTATTTA
* * *
251400 GTATCGATACCC-CTACTATGGTATCGATACTACCCTACTATGGTATCGATACCCCGATTT-AAT
1 GTATCGATACCCTC-ACCATGGTATCGATACTACCATACTATGGTACCGATACCCC-ATTTCAAT
*
251463 ATTGATACCAAAATTAGCTTCGATGTAGCCTG
64 ATCGATACCAAAATTAGCTTCGATGTAGCCTG
* * * * *
251495 GTATCGATACCCTCACCATGGTATCGATATTACTATATTATGGTACCGATACCCCCTTTCAGTAT
1 GTATCGATACCCTCACCATGGTATCGATACTACCATACTATGGTACCGATACCCCATTTCAATAT
* **
251560 CGATACCAAAATTAGGTTCGATGTTTCCTG
66 CGATACCAAAATTAGCTTCGATGTAGCCTG
** * *
251590 GTATTAATACCCTTACCATGGTATTGATACTAC
1 GTATCGATACCCTCACCATGGTATCGATACTAC
251623 ATCGCTTGGT
Statistics
Matches: 109, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
94 3 0.03
95 105 0.96
96 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (95 bp):
GTATCGATACCCTCACCATGGTATCGATACTACCATACTATGGTACCGATACCCCATTTCAATAT
CGATACCAAAATTAGCTTCGATGTAGCCTG
Found at i:261497 original size:13 final size:13
Alignment explanation
Indices: 261479--261503 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
261469 TCTTAGTTCT
261479 CTATAGTAATATG
1 CTATAGTAATATG
261492 CTATAGTAATAT
1 CTATAGTAATAT
261504 CAATAGCATC
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:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
CTATAGTAATATG
Found at i:264798 original size:20 final size:22
Alignment explanation
Indices: 264752--264808 Score: 82
Period size: 20 Copynumber: 2.6 Consensus size: 22
264742 ACCATCGACA
264752 TGACCATTGACTTTGACTAGAGT
1 TGACCATTGACTTTGACTA-AGT
*
264775 TGACCATTGACTTTGA-T-CGT
1 TGACCATTGACTTTGACTAAGT
264795 TGACCATTGACTTT
1 TGACCATTGACTTT
264809 AACCAAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 16 0.48
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (22 bp):
TGACCATTGACTTTGACTAAGT
Found at i:273500 original size:14 final size:14
Alignment explanation
Indices: 273483--273562 Score: 83
Period size: 14 Copynumber: 5.7 Consensus size: 14
273473 AAGTGAATGG
273483 GTTGACTC-GGACGA
1 GTTGACTCAGG-CGA
*
273497 GTTGACTCATGCGA
1 GTTGACTCAGGCGA
* *
273511 GTTGTCTC-GAACGA
1 GTTGACTCAG-GCGA
*
273525 GTTGACTCAGGCAA
1 GTTGACTCAGGCGA
273539 GTTGACTCAGGCGA
1 GTTGACTCAGGCGA
*
273553 GTTGAATCAG
1 GTTGACTCAG
273563 TTCAGACGGG
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
14 52 0.96
15 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (14 bp):
GTTGACTCAGGCGA
Found at i:273524 original size:28 final size:28
Alignment explanation
Indices: 273483--273546 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 28
273473 AAGTGAATGG
* * *
273483 GTTGACTCGGACGAGTTGACTCATGCGA
1 GTTGACTCGAACGAGTTGACTCAGGCAA
*
273511 GTTGTCTCGAACGAGTTGACTCAGGCAA
1 GTTGACTCGAACGAGTTGACTCAGGCAA
273539 GTTGACTC
1 GTTGACTC
273547 AGGCGAGTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.27
Consensus pattern (28 bp):
GTTGACTCGAACGAGTTGACTCAGGCAA
Found at i:281599 original size:19 final size:19
Alignment explanation
Indices: 281577--281619 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
281567 AAATTTTGGC
*
281577 TTTTTTGTG-TTTTTATGTT
1 TTTTTTGTGCCTTTT-TGTT
*
281596 TTTTTTTTGCCTTTTTGTT
1 TTTTTTGTGCCTTTTTGTT
281615 TTTTT
1 TTTTT
281620 GTTTTTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.02, C:0.05, G:0.12, T:0.81
Consensus pattern (19 bp):
TTTTTTGTGCCTTTTTGTT
Found at i:281600 original size:27 final size:26
Alignment explanation
Indices: 281570--281625 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 26
281560 TTTTTTGAAA
*
281570 TTTTGGCTTTTTTGTGTTTTTATGTTTTT
1 TTTTGGCCTTTTTGT-TTTTT-TG-TTTT
*
281599 TTTTTGCCTTTTTGTTTTTTTGTTTT
1 TTTTGGCCTTTTTGTTTTTTTGTTTT
281625 T
1 T
281626 GAAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 2 0.08
28 5 0.20
29 13 0.52
ACGTcount: A:0.02, C:0.05, G:0.14, T:0.79
Consensus pattern (26 bp):
TTTTGGCCTTTTTGTTTTTTTGTTTT
Found at i:281610 original size:21 final size:21
Alignment explanation
Indices: 281577--281626 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
281567 AAATTTTGGC
**
281577 TTTTTTGTGTTTTTATGTTTT
1 TTTTTTGCCTTTTTATGTTTT
* *
281598 TTTTTTGCCTTTTTGTTTTTT
1 TTTTTTGCCTTTTTATGTTTT
281619 TGTTTTTG
1 T-TTTTTG
281627 AAAAAAAATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.02, C:0.04, G:0.14, T:0.80
Consensus pattern (21 bp):
TTTTTTGCCTTTTTATGTTTT
Found at i:283258 original size:44 final size:45
Alignment explanation
Indices: 283199--283287 Score: 135
Period size: 44 Copynumber: 2.0 Consensus size: 45
283189 TCTGCCATTT
* * *
283199 TTAATTAACTAATTTAATTATTATTAATTTAAAACTCTTTTTAAA
1 TTAAATAACTAATTTAATCATTACTAATTTAAAACTCTTTTTAAA
*
283244 TTAAATAA-TAATTTAATCATTACTAATTTAAAACTTTTTTTAAA
1 TTAAATAACTAATTTAATCATTACTAATTTAAAACTCTTTTTAAA
283288 AAATAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 33 0.82
45 7 0.17
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (45 bp):
TTAAATAACTAATTTAATCATTACTAATTTAAAACTCTTTTTAAA
Found at i:283987 original size:30 final size:30
Alignment explanation
Indices: 283953--284018 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
283943 TTGTTTTTAG
* *
283953 AATAAAAGATAAAGATAAAATAACTAATTA
1 AATAAAAGATAAAGATAAAATAAATAAATA
* *
283983 AATAAAAGATAAGGATATAATAAATAAATA
1 AATAAAAGATAAAGATAAAATAAATAAATA
284013 AATAAA
1 AATAAA
284019 TTTAAAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.23
Consensus pattern (30 bp):
AATAAAAGATAAAGATAAAATAAATAAATA
Found at i:284641 original size:15 final size:16
Alignment explanation
Indices: 284621--284653 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
284611 CTTAGCTTCT
*
284621 TTGAAAATAAAAA-AA
1 TTGAAAACAAAAAGAA
284636 TTGAAAACAAAAAGAA
1 TTGAAAACAAAAAGAA
284652 TT
1 TT
284654 TTTTTATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.67, C:0.03, G:0.09, T:0.21
Consensus pattern (16 bp):
TTGAAAACAAAAAGAA
Found at i:286258 original size:325 final size:332
Alignment explanation
Indices: 285630--286276 Score: 914
Period size: 325 Copynumber: 2.0 Consensus size: 332
285620 CATGAATATC
* * * * *
285630 AACTTTATATTAATATTATTTTATTATTGTTCCGACAATAATAATTGACTAGGGATATTTGGGTA
1 AACTTCATATTAATATTATTTTATTATCGTTCCGACAATAATAATCGACTAGGGATATTTGAGAA
* * *
285695 TAATTAACAATAATATTCAAGGATATTAATATACAAAAAGCATGTAAATAATAATAATAAATACA
66 TAATTAAAAATAATATTCAAGGATATTAATATACAAAAAGAATGTAAATAATAACAATAAATACA
* ** * * *
285760 ATAATCAAAATATCATGTCCATACAATATAGGCTTGGGGCACTATTTATCAATAGATGCTTTGGT
131 ATAATCAAAATATCATGTCCATACAATATAGGCCTAAGGCAATATTTACCAACAGATGCTTTGGT
** * *
285825 TGTCGAGTTACAGATTAGGCCGACTTTGTCGCAGCATATTAAGGAGTTGGAACCTGCCAATATAT
196 TGTCGAGTTACAGATTAGGCCGACTTTGTCGCAGCATATTAAGGAGTTACAACATGCCAATAGAT
* * *
285890 TGTTTGGAGCGAACATTCAGTTGGTTCGAGATGGTTCAGGTGATGGTTTTGCTTTTGATGTTGAT
261 TGTTTAGAGAGAACATTCAGTTGGTTCGAGATGGTTCAGGTGATGATTTTGCTTTTGATGTTGAT
285955 GGTGTCA
326 GGTGTCA
*
285962 AACTTCATATTAATCTTATTTTATTATCGTTCTC-ACAATAATAATCGACTAGGGATATTT-AGA
1 AACTTCATATTAATATTATTTTATTATCGTTC-CGACAATAATAATCGACTAGGGATATTTGAGA
* *
286025 ATAATTAAAAATAATATTCAAGGATATTAATATACAAAAAGAATGTACATGATAACAATAAATAC
65 ATAATTAAAAATAATATTCAAGGATATTAATATACAAAAAGAATGTAAATAATAACAATAAATAC
* * *
286090 AATAATCAAAATATCATGTTCATAC-A-ATAGGCCTAAGGCAATA-TTGCCAACGGATGCTTTGG
130 AATAATCAAAATATCATGTCCATACAATATAGGCCTAAGGCAATATTTACCAACAGATGCTTTGG
* ** * **
286152 -T-T-GAGTTACTGATTAGGCCGACTTTGTCGCAGTGTATTAAGGAGTTACAATATTTCAATAGA
195 TTGTCGAGTTACAGATTAGGCCGACTTTGTCGCAGCATATTAAGGAGTTACAACATGCCAATAGA
* *
286214 TTGTTTAGAGAGAAGATTCAGTTGGTTCGAGATGGTTTAGGTGATGATTTTGCTTTTGATGTT
260 TTGTTTAGAGAGAACATTCAGTTGGTTCGAGATGGTTCAGGTGATGATTTTGCTTTTGATGTT
286277 TGAACATGTT
Statistics
Matches: 279, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
325 108 0.39
326 1 0.00
327 1 0.00
328 15 0.05
329 13 0.05
330 1 0.00
331 85 0.30
332 54 0.19
333 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (332 bp):
AACTTCATATTAATATTATTTTATTATCGTTCCGACAATAATAATCGACTAGGGATATTTGAGAA
TAATTAAAAATAATATTCAAGGATATTAATATACAAAAAGAATGTAAATAATAACAATAAATACA
ATAATCAAAATATCATGTCCATACAATATAGGCCTAAGGCAATATTTACCAACAGATGCTTTGGT
TGTCGAGTTACAGATTAGGCCGACTTTGTCGCAGCATATTAAGGAGTTACAACATGCCAATAGAT
TGTTTAGAGAGAACATTCAGTTGGTTCGAGATGGTTCAGGTGATGATTTTGCTTTTGATGTTGAT
GGTGTCA
Found at i:291777 original size:14 final size:14
Alignment explanation
Indices: 291739--291777 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
291729 TTGTCATTTT
*
291739 TTTTTTC-TTTTCC
1 TTTTTTCTTTTTCA
*
291752 TCTTTTCTTTTTCA
1 TTTTTTCTTTTTCA
291766 TTTTTTCTTTTT
1 TTTTTTCTTTTT
291778 GATAAAAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 6 0.27
14 16 0.73
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTCTTTTTCA
Found at i:296151 original size:13 final size:13
Alignment explanation
Indices: 296141--296304 Score: 67
Period size: 14 Copynumber: 12.4 Consensus size: 13
296131 AAATTATAAG
296141 ATATAAATATATA
1 ATATAAATATATA
296154 ATATAAATA-AT-
1 ATATAAATATATA
*
296165 ATAAAAATATAT-
1 ATATAAATATATA
* *
296177 TTATATAT-TAATA
1 ATATAAATAT-ATA
296190 ATATTAAA-ATAT-
1 ATA-TAAATATATA
*
296202 -TA-AAATATAAA
1 ATATAAATATATA
* *
296213 AAATATATATATA
1 ATATAAATATATA
*
296226 TATATATATATATA
1 -ATATAAATATATA
*
296240 TATATATATATATA
1 -ATATAAATATATA
*
296254 ACTACGTAAACAT-TA
1 A-TA--TAAATATATA
*
296269 TATATAAAAATATA
1 -ATATAAATATATA
296283 ATAATAGTAATAGTATA
1 AT-ATA--AATA-TATA
296300 ATATA
1 ATATA
296305 TAATGTAAGA
Statistics
Matches: 117, Mismatches: 15, Indels: 35
0.70 0.09 0.21
Matches are distributed among these distances:
9 3 0.03
10 3 0.03
11 11 0.09
12 12 0.10
13 29 0.25
14 37 0.32
15 4 0.03
16 12 0.10
17 6 0.05
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
ATATAAATATATA
Found at i:296154 original size:8 final size:8
Alignment explanation
Indices: 296141--296254 Score: 70
Period size: 8 Copynumber: 13.8 Consensus size: 8
296131 AAATTATAAG
296141 ATATAAAT
1 ATATAAAT
296149 ATAT-AAT
1 ATATAAAT
*
296156 ATAAATAAT
1 ATATA-AAT
*
296165 ATAAAAAT
1 ATATAAAT
**
296173 ATATTTAT
1 ATATAAAT
*
296181 ATATTAAT
1 ATATAAAT
296189 AATATTAAA-
1 -ATA-TAAAT
296198 ATATTAAAAT
1 ATA-T-AAAT
*
296208 ATAAAAAAT
1 AT-ATAAAT
*
296217 ATATATAT
1 ATATAAAT
*
296225 ATATATAT
1 ATATAAAT
*
296233 ATATATAT
1 ATATAAAT
*
296241 ATATATAT
1 ATATAAAT
296249 ATATAA
1 ATATAA
296255 CTACGTAAAC
Statistics
Matches: 89, Mismatches: 10, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
7 6 0.07
8 57 0.64
9 20 0.22
10 5 0.06
11 1 0.01
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
ATATAAAT
Found at i:296173 original size:17 final size:17
Alignment explanation
Indices: 296153--296219 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
296143 ATAAATATAT
296153 AATATAAATAATATAAA
1 AATATAAATAATATAAA
** *
296170 AATATATTTATATATTAAT
1 AATATAAATA-ATA-TAAA
* *
296189 AATATTAA-AATATTAA
1 AATATAAATAATATAAA
*
296205 AATATAAAAAATATA
1 AATATAAATAATATA
296220 TATATATATA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
16 9 0.24
17 16 0.43
18 4 0.11
19 8 0.22
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AATATAAATAATATAAA
Found at i:296272 original size:2 final size:2
Alignment explanation
Indices: 296215--296253 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
296205 AATATAAAAA
296215 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
296254 ACTACGTAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:298028 original size:39 final size:40
Alignment explanation
Indices: 297942--298043 Score: 143
Period size: 39 Copynumber: 2.6 Consensus size: 40
297932 ATAGTGCTAT
*
297942 ACATAAGGTTGTGCCCACCATATGCACCAAAGTACATTAC
1 ACATAAGGTCGTGCCCACCATATGCACCAAAGTACATTAC
* ** *
297982 ACATAAGGTCGTGCCCACTATATGCA-GGAATTACATTAC
1 ACATAAGGTCGTGCCCACCATATGCACCAAAGTACATTAC
*
298021 ACATAAGGTCGTTCCCACCATAT
1 ACATAAGGTCGTGCCCACCATAT
298044 TACACTTAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 31 0.56
40 24 0.44
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (40 bp):
ACATAAGGTCGTGCCCACCATATGCACCAAAGTACATTAC
Found at i:300278 original size:30 final size:31
Alignment explanation
Indices: 300218--300292 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
300208 TTGGGGCCTG
*
300218 AGAGCCTACCCAAGAAAGTTCTCAGGGCCAC
1 AGAGCCTACCCAAGAAAGATCTCAGGGCCAC
* *
300249 GGGGCCTACCCAAGAAAGATCTC-GGGCCAC
1 AGAGCCTACCCAAGAAAGATCTCAGGGCCAC
300279 AGAGCCTACCCAAG
1 AGAGCCTACCCAAG
300293 GTCACCTTAG
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 19 0.49
31 20 0.51
ACGTcount: A:0.31, C:0.33, G:0.25, T:0.11
Consensus pattern (31 bp):
AGAGCCTACCCAAGAAAGATCTCAGGGCCAC
Found at i:307807 original size:31 final size:30
Alignment explanation
Indices: 307725--307813 Score: 160
Period size: 30 Copynumber: 2.9 Consensus size: 30
307715 AATTACCATT
*
307725 AAACCAAGACACCTAACCTTATCGTCTTTC
1 AAACCAAGACACCTAACCTTATCATCTTTC
307755 AAACCAAGACACCTAACCTTATCATCTTTC
1 AAACCAAGACACCTAACCTTATCATCTTTC
307785 AAACCAAGACACCTAAACCTTATCATCTT
1 AAACCAAGACACCT-AACCTTATCATCTT
307814 CCATAAGTCA
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 43 0.75
31 14 0.25
ACGTcount: A:0.37, C:0.33, G:0.04, T:0.26
Consensus pattern (30 bp):
AAACCAAGACACCTAACCTTATCATCTTTC
Found at i:308661 original size:45 final size:46
Alignment explanation
Indices: 308611--308739 Score: 188
Period size: 45 Copynumber: 2.8 Consensus size: 46
308601 TGATTAGACA
* * *
308611 TTACCATACTGTAAGGATGCACCATCCTGTAAATCGGTAATTGG-T
1 TTACCATCCTGTAAGGATGCACCAACCTGTATATCGGTAATTGGAT
308656 TTACCATCCTGTAAGGATGCACCAACCTGTATATCGGTAATTGGAT
1 TTACCATCCTGTAAGGATGCACCAACCTGTATATCGGTAATTGGAT
* * * *
308702 TTATCATCCGGTAAGGATGCACCAGCCTATATATCGGT
1 TTACCATCCTGTAAGGATGCACCAACCTGTATATCGGT
308740 TACTCTTCCT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
45 41 0.54
46 35 0.46
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (46 bp):
TTACCATCCTGTAAGGATGCACCAACCTGTATATCGGTAATTGGAT
Found at i:308911 original size:4 final size:4
Alignment explanation
Indices: 308902--309143 Score: 475
Period size: 4 Copynumber: 60.2 Consensus size: 4
308892 CAATATATAC
308902 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
308950 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
308998 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
309046 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
309094 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -ACAT
309143 A
1 A
309144 TCATCGATAC
Statistics
Matches: 237, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
4 233 0.98
5 4 0.02
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:309532 original size:20 final size:21
Alignment explanation
Indices: 309499--309551 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
309489 TTCGAAAAAA
309499 AGTTAACGAGTCAAAGTCAAC
1 AGTTAACGAGTCAAAGTCAAC
* *
309520 AGTTAAC-AGTCAAATTCAAT
1 AGTTAACGAGTCAAAGTCAAC
*
309540 AGTCAACGAGTC
1 AGTTAACGAGTC
309552 GGGTCAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.23
Consensus pattern (21 bp):
AGTTAACGAGTCAAAGTCAAC
Found at i:311444 original size:24 final size:24
Alignment explanation
Indices: 311412--311469 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
311402 TACGACTTGC
311412 TTTTGGAAAGATAAGCTTTTCAAG
1 TTTTGGAAAGATAAGCTTTTCAAG
311436 TTTTGGAAAGATAAGCTTTTCAAG
1 TTTTGGAAAGATAAGCTTTTCAAG
*
311460 TTTTGAAAAG
1 TTTTGGAAAG
311470 TTTTCCTTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (24 bp):
TTTTGGAAAGATAAGCTTTTCAAG
Found at i:325585 original size:27 final size:26
Alignment explanation
Indices: 325555--325611 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
325545 TATTTTAGCC
325555 ATTTCAAAGCTTGAGGGT-GTTTTGATT
1 ATTTCAAAGCTTG-GGGTAGTTTTG-TT
** *
325582 ATTTTGAAGCTTGGGGTATTTTTGTT
1 ATTTCAAAGCTTGGGGTAGTTTTGTT
325608 ATTT
1 ATTT
325612 TGGGTTTTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 10 0.38
27 16 0.62
ACGTcount: A:0.19, C:0.05, G:0.25, T:0.51
Consensus pattern (26 bp):
ATTTCAAAGCTTGGGGTAGTTTTGTT
Found at i:325609 original size:26 final size:27
Alignment explanation
Indices: 325561--325613 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
325551 AGCCATTTCA
325561 AAGCTTGAGGGTGTTTTGATTATTTTG
1 AAGCTTGAGGGTGTTTTGATTATTTTG
*
325588 AAGCTTG-GGGTATTTTTG-TTATTTTG
1 AAGCTTGAGGGT-GTTTTGATTATTTTG
325614 GGTTTTAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 12 0.50
27 12 0.50
ACGTcount: A:0.17, C:0.04, G:0.28, T:0.51
Consensus pattern (27 bp):
AAGCTTGAGGGTGTTTTGATTATTTTG
Found at i:325691 original size:26 final size:27
Alignment explanation
Indices: 325623--325692 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
325613 GGGTTTTAGG
*
325623 GGTATTTCGATCATTTTATAATTCAAT
1 GGTATTTTGATCATTTTATAATTCAAT
* * *
325650 GGTATTTTGGA-AATTTTATAGTTTAA-
1 GGTATTTT-GATCATTTTATAATTCAAT
325676 GGTATTTTGATCATTTT
1 GGTATTTTGATCATTTT
325693 GGAGTCTAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
25 2 0.06
26 13 0.36
27 19 0.53
28 2 0.06
ACGTcount: A:0.27, C:0.06, G:0.16, T:0.51
Consensus pattern (27 bp):
GGTATTTTGATCATTTTATAATTCAAT
Found at i:328175 original size:27 final size:27
Alignment explanation
Indices: 328145--328202 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
328135 ACTATATTTC
328145 CTTAAAAGAAAGAATACTTAGGATATT
1 CTTAAAAGAAAGAATACTTAGGATATT
**** *
328172 CTTAGTTTAAAGAATAGTTAGGATATT
1 CTTAAAAGAAAGAATACTTAGGATATT
328199 CTTA
1 CTTA
328203 GTTTGATCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (27 bp):
CTTAAAAGAAAGAATACTTAGGATATT
Found at i:328203 original size:27 final size:27
Alignment explanation
Indices: 328153--328206 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
328143 TCCTTAAAAG
328153 AAAGAATACTTAGGATATTCTTAGTTT
1 AAAGAATACTTAGGATATTCTTAGTTT
*
328180 AAAGAATAGTTAGGATATTCTTAGTTT
1 AAAGAATACTTAGGATATTCTTAGTTT
328207 GATCTATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.37, C:0.06, G:0.17, T:0.41
Consensus pattern (27 bp):
AAAGAATACTTAGGATATTCTTAGTTT
Found at i:332117 original size:24 final size:23
Alignment explanation
Indices: 332073--332117 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
332063 CAAGAATGAA
*
332073 TGATGATTTTCGGAATATTTAAT
1 TGATGATTTTCGCAATATTTAAT
* *
332096 TGATGCATTTTCTCAATTTTTA
1 TGATG-ATTTTCGCAATATTTA
332118 TTTTTGATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.27, C:0.09, G:0.13, T:0.51
Consensus pattern (23 bp):
TGATGATTTTCGCAATATTTAAT
Found at i:332720 original size:187 final size:187
Alignment explanation
Indices: 332315--333787 Score: 2273
Period size: 187 Copynumber: 8.0 Consensus size: 187
332305 CTGAGCTTTG
* * *
332315 AAAAATATGTATAACTTGTTTAAAGACTCAATAACACTTAAAATTACTTTTCACACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
332380 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAAT-AAAAA
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
* * *
332444 TAATTAATAATTCATATTATATCAAAACCAAATATTAGTTCAACGGTTAGTATGCTT
131 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTGTTAGCATGCTT
* *
332501 AAAAACATGTATAACTTATTTAAAGACTCAATAAAACTTAAGATTACTTTTCAAACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
* *
332566 ACTTGAAAATGTTCTATGACAAATTTTCATAGTTTTATGATA-ATGAAAATTTTAACAATAAAAA
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGA-ACATGCAAATTTTAACAATAAAAA
* * *
332630 TTAATTAAGAATTCATATTATATCAAAACCAAATATTGGTTCAACTGATAGCATGCTT
130 ATAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTGTTAGCATGCTT
332688 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACAC--------T
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
332745 --TTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
* * *
332808 TAATTGATAATTCATATTATATCAAAACCAAATATTGGCTCAACAGTTAGCATGCTT
131 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTGTTAGCATGCTT
*
332865 AAAAACATGTATAACTTGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
*
332930 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAAAAAAT-CAAATTTTAACAATAAAA
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATG--AACATGCAAATTTTAACAATAAAA
* * *
332994 ATTAATTAATAATTCATATTATATGAAAACCAAATATTGGTTCAACTTTTAGCATGCTT
129 AATAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTGTTAGCATGCTT
333053 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
* *
333118 ACTTGAAAGTGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATGTTAACAATAAAAAA
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
*
333183 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTATTAGCATGCTT
131 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTGTTAGCATGCTT
* *
333240 AAAAACTTGTATAACTTGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACAC--------T
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
333297 --TTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
* * * * * *
333360 TAATTAATTATTCATATTATATAAAAACCAAATATTTGTTCATCAGTTAGCAAGCTT
131 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTGTTAGCATGCTT
333417 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
* * *
333482 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAAAATGCAAATTTTAACATTAAAAAT
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
* *
333547 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTCTTAGCGTGCTT
131 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTGTTAGCATGCTT
* * *
333604 AAAAATATGTATAACTTGTTTAAAGACTTAATAAAACTTAAGATTACTTTTCACACATAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
* * * *
333669 ACTTGAAAATATTTTATGACAAATTTTCATAGTTTTATGAAAATGTAAATTATAACAAT---AAA
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
* * * **
333731 -AATTAACAATTCATGA-TATATCAAAATCAAATATTTGTTCAACAATTAGCATGCTT
131 TAATTAATAATTCAT-ATTATATCAAAACCAAATATTGGTTCAACTGTTAGCATGCTT
333787 A
1 A
333788 GATTTATTAA
Statistics
Matches: 1184, Mismatches: 76, Indels: 57
0.90 0.06 0.04
Matches are distributed among these distances:
176 1 0.00
177 330 0.28
179 2 0.00
183 49 0.04
184 3 0.00
185 2 0.00
186 119 0.10
187 501 0.42
188 173 0.15
189 4 0.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (187 bp):
AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTGTTAGCATGCTT
Found at i:332965 original size:364 final size:366
Alignment explanation
Indices: 332315--333787 Score: 2115
Period size: 364 Copynumber: 4.0 Consensus size: 366
332305 CTGAGCTTTG
* * *
332315 AAAAATATGTATAACTTGTTTAAAGACTCAATAACACTTAAAATTACTTTTCACACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACAC------A-T
332380 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAAT-AAAAA
59 A-TTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
* * *
332444 TAATTAATAATTCATATTATATCAAAACCAAATATTAGTTCAACGGTTAGTATGCTTAAAAACAT
123 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACAGTTAGCATGCTTAAAAACAT
* * *
332509 GTATAACTTATTTAAAGACTCAATAAAACTTAAGATTACTTTTCAAACTTAAAAATTACTTGAAA
188 GTATAACTTGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGAAA
* * * *
332574 ATGTTCTATGACAAATTTTCATAGTTTTATGATAATGAAAATTTTAACAATAAAAATTAATTAAG
253 ATGTTTTATGACAAATTTTCATAGTTTTATGAAAATGCAAATTTTAACAATAAAAATTAATTAAT
332639 AATTCATATTATATCAAAACCAAATATTGGTTCAACTGATAGCATGCTT
318 AATTCATATTATATCAAAACCAAATATTGGTTCAACTGATAGCATGCTT
332688 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACAC-T-TTGAAA
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACATATTGAAA
*
332751 ATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAATAATTGAT
66 ATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAATAATTAAT
*
332816 AATTCATATTATATCAAAACCAAATATTGGCTCAACAGTTAGCATGCTTAAAAACATGTATAACT
131 AATTCATATTATATCAAAACCAAATATTGGTTCAACAGTTAGCATGCTTAAAAACATGTATAACT
332881 TGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGAAAATGTTTTA
196 TGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGAAAATGTTTTA
332946 TGACAAATTTTCATAGTTTTATGAAAAAAT-CAAATTTTAACAATAAAAATTAATTAATAATTCA
261 TGACAAATTTTCATAGTTTTATG--AAAATGCAAATTTTAACAATAAAAATTAATTAATAATTCA
* **
333010 TATTATATGAAAACCAAATATTGGTTCAACTTTTAGCATGCTT
324 TATTATATCAAAACCAAATATTGGTTCAACTGATAGCATGCTT
333053 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACAC------A-T
* *
333118 ACTTGAAAGTGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATGTTAACAATAAAAAA
59 A-TTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
*
333183 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTA-TTAGCATGCTTAAAAACT
123 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAAC-AGTTAGCATGCTTAAAAACA
333247 TGTATAACTTGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACAC--------T--TTGAA
187 TGTATAACTTGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGAA
* *
333302 AATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAATAATTAA
252 AATGTTTTATGACAAATTTTCATAGTTTTATGAAAATGCAAATTTTAACAATAAAAATTAATTAA
* * * * * * *
333367 TTATTCATATTATATAAAAACCAAATATTTGTTCATCAGTTAGCAAGCTT
317 TAATTCATATTATATCAAAACCAAATATTGGTTCAACTGATAGCATGCTT
333417 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACAC------A-T
* * *
333482 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAAAATGCAAATTTTAACATTAAAAAT
59 A-TTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAA
** * *
333547 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTCTTAGCGTGCTTAAAAATAT
123 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACAGTTAGCATGCTTAAAAACAT
* * *
333612 GTATAACTTGTTTAAAGACTTAATAAAACTTAAGATTACTTTTCACACATAAAAATTACTTGAAA
188 GTATAACTTGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGAAA
* * * *
333677 ATATTTTATGACAAATTTTCATAGTTTTATGAAAATGTAAATTATAACAAT--AAA--AATTAAC
253 ATGTTTTATGACAAATTTTCATAGTTTTATGAAAATGCAAATTTTAACAATAAAAATTAATTAAT
* * *
333738 AATTCATGA-TATATCAAAATCAAATATTTGTTCAAC-AATTAGCATGCTT
318 AATTCAT-ATTATATCAAAACCAAATATTGGTTCAACTGA-TAGCATGCTT
333787 A
1 A
333788 GATTTATTAA
Statistics
Matches: 1017, Mismatches: 55, Indels: 59
0.90 0.05 0.05
Matches are distributed among these distances:
363 61 0.06
364 457 0.45
365 166 0.16
366 4 0.00
367 1 0.00
370 46 0.05
371 1 0.00
372 4 0.00
373 54 0.05
374 53 0.05
375 169 0.17
376 1 0.00
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (366 bp):
AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACATATTGAAA
ATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAATAATTAAT
AATTCATATTATATCAAAACCAAATATTGGTTCAACAGTTAGCATGCTTAAAAACATGTATAACT
TGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGAAAATGTTTTA
TGACAAATTTTCATAGTTTTATGAAAATGCAAATTTTAACAATAAAAATTAATTAATAATTCATA
TTATATCAAAACCAAATATTGGTTCAACTGATAGCATGCTT
Found at i:333362 original size:552 final size:549
Alignment explanation
Indices: 332315--333787 Score: 2458
Period size: 552 Copynumber: 2.7 Consensus size: 549
332305 CTGAGCTTTG
* * *
332315 AAAAATATGTATAACTTGTTTAAAGACTCAATAACACTTAAAATTACTTTTCACACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
*
332380 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAA-
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAAAATGCAAATTTTAACAATAAAAAT
* ** *
332444 TAATTAATAATTCATATTATATCAAAACCAAATATTAGTTCAACGGTTAGTATGCTTAAAAACAT
131 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTCTTAGCATGCTTAAAAACAT
* *
332509 GTATAACTTATTTAAAGACTCAATAAAACTTAAGATTACTTTTCAAACTTAAAAATTACTTGAAA
196 GTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGAAA
* * *
332574 ATGTTCTATGACAAATTTTCATAGTTTTATGATAATGAAAATTTTAACAATAAAAATTAATTAAG
261 ATGTTTTATGACAAATTTTCATAGTTTTATGA-AATGAAAA-TTTAACAATAAAAAATAATTAAC
332639 AATTCATATTATATCAAAACCAAATATTGGTTCAACTGA-TAGCATGCTTAAAAACATGTATAAC
324 AATTCATATTATATCAAAACCAAATATTGGTTCAACT-ATTAGCATGCTTAAAAACATGTATAAC
*
332703 TTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTTGAAAATGTTTTATGACAAATT
388 TTGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTTGAAAATGTTTTATGACAAATT
* *
332768 TTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAATAATTGATAATTCATATTATATCAA
453 TTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAATAATTAATAATTCATATTATATAAA
*
332833 AACCAAATATTGGCTCAACAGTTAGCATGCTT
518 AACCAAATATTGGCTCAACAGTTAGCAAGCTT
*
332865 AAAAACATGTATAACTTGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
332930 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAAAAAAT-CAAATTTTAACAATAAAA
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATG--AAAATGCAAATTTTAACAATAAAA
* *
332994 ATTAATTAATAATTCATATTATATGAAAACCAAATATTGGTTCAACTTTTAGCATGCTTAAAAAC
129 ATTAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTCTTAGCATGCTTAAAAAC
333059 ATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGA
194 ATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGA
* *
333124 AAGTGTTTTATGACAAATTTTCATAGTTTTATGAACATGCAAATGTTAACAATAAAAAATAATTA
259 AAATGTTTTATGACAAATTTTCATAGTTTTATGAA-ATGAAAAT-TTAACAATAAAAAATAATTA
* *
333189 ATAATTCATATTATATCAAAACCAAATATTGGTTCAACTATTAGCATGCTTAAAAACTTGTATAA
322 ACAATTCATATTATATCAAAACCAAATATTGGTTCAACTATTAGCATGCTTAAAAACATGTATAA
333254 CTTGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTTGAAAATGTTTTATGACAAAT
387 CTTGTTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTTGAAAATGTTTTATGACAAAT
*
333319 TTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAATAATTAATTATTCATATTATATAA
452 TTTCATAGTTTTATGAACATGCAAATTTTAACAATAAAAAATAATTAATAATTCATATTATATAA
* * *
333384 AAACCAAATATTTGTTCATCAGTTAGCAAGCTT
517 AAACCAAATATTGGCTCAACAGTTAGCAAGCTT
333417 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
1 AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
*
333482 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAAAATGCAAATTTTAACATTAAAAAT
66 ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAAAATGCAAATTTTAACAATAAAAAT
* *
333547 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTCTTAGCGTGCTTAAAAATAT
131 TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTCTTAGCATGCTTAAAAACAT
* *
333612 GTATAACTTGTTTAAAGACTTAATAAAACTTAAGATTACTTTTCACACATAAAAATTACTTGAAA
196 GTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGAAA
* *
333677 ATATTTTATGACAAATTTTCATAGTTTTATGAAAATGTAAATTATAACAAT---AAA-AATTAAC
261 ATGTTTTATGACAAATTTTCATAGTTTTATG-AAATGAAAATT-TAACAATAAAAAATAATTAAC
* * *
333738 AATTCATGA-TATATCAAAATCAAATATTTGTTCAACAATTAGCATGCTTA
324 AATTCAT-ATTATATCAAAACCAAATATTGGTTCAACTATTAGCATGCTTA
333788 GATTTATTAA
Statistics
Matches: 872, Mismatches: 41, Indels: 23
0.93 0.04 0.02
Matches are distributed among these distances:
547 51 0.06
548 4 0.00
550 106 0.12
551 208 0.24
552 503 0.58
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.37
Consensus pattern (549 bp):
AAAAACATGTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATT
ACTTGAAAATGTTTTATGACAAATTTTCATAGTTTTATGAAAATGCAAATTTTAACAATAAAAAT
TAATTAATAATTCATATTATATCAAAACCAAATATTGGTTCAACTCTTAGCATGCTTAAAAACAT
GTATAACTTGTTTAAAGACTCAATAAAACTTAAGATTACTTTTCACACTTAAAAATTACTTGAAA
ATGTTTTATGACAAATTTTCATAGTTTTATGAAATGAAAATTTAACAATAAAAAATAATTAACAA
TTCATATTATATCAAAACCAAATATTGGTTCAACTATTAGCATGCTTAAAAACATGTATAACTTG
TTTAAAAACTCAATAAAACTTAAGATTACTTTTCACACTTTGAAAATGTTTTATGACAAATTTTC
ATAGTTTTATGAACATGCAAATTTTAACAATAAAAAATAATTAATAATTCATATTATATAAAAAC
CAAATATTGGCTCAACAGTTAGCAAGCTT
Found at i:348791 original size:138 final size:138
Alignment explanation
Indices: 348543--348801 Score: 380
Period size: 138 Copynumber: 1.9 Consensus size: 138
348533 TACACCTAAG
* * *
348543 TGTTGAAATGGAAATTCAAAAACTCATTATGAATTCCATTGATGCACACATAGTGCCGAAAGTAC
1 TGTTGAAATGGAAATTCAAAAACTCATTATAAATTCCATGGATGCACACATAGTGCCAAAAGTAC
* * *
348608 ATATAGTACTGATACGAAAATGCACCGTTATGCATTTAACAAAATCGATCGATAACTTTTATACA
66 ATATAGTACTAATACAAAAATGCACCATTATGCATTTAACAAAATCGATCGATAACTTTTATACA
348673 TAATTGTA
131 TAATTGTA
* * *
348681 TGTTGAAATGGTAATTCACAAACTCATTATAAATAT-CATGGTTGCACATC-TAGTGCCAAAAGT
1 TGTTGAAATGGAAATTCAAAAACTCATTATAAAT-TCCATGGATGCACA-CATAGTGCCAAAAGT
*
348744 ACATATAGTACTAATACAAAAATGCACCATTATGCA-TTACATAAAATCGATCGATAAC
64 ACATATAGTACTAATACAAAAATGCACCATTATGCATTTA-ACAAAATCGATCGATAAC
348802 CATTATATAC
Statistics
Matches: 108, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
137 3 0.03
138 103 0.95
139 2 0.02
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.30
Consensus pattern (138 bp):
TGTTGAAATGGAAATTCAAAAACTCATTATAAATTCCATGGATGCACACATAGTGCCAAAAGTAC
ATATAGTACTAATACAAAAATGCACCATTATGCATTTAACAAAATCGATCGATAACTTTTATACA
TAATTGTA
Found at i:349484 original size:21 final size:20
Alignment explanation
Indices: 349444--349493 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
349434 CTTCCTCTTG
349444 GTATCGATACCTACACATCA
1 GTATCGATACCTACACATCA
349464 GTATCGATA-CTACTTACATCA
1 GTATCGATACCTAC--ACATCA
349485 GTATCGATA
1 GTATCGATA
349494 TTGTTCATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.14
20 9 0.32
21 15 0.54
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (20 bp):
GTATCGATACCTACACATCA
Found at i:358901 original size:65 final size:65
Alignment explanation
Indices: 358790--358949 Score: 191
Period size: 65 Copynumber: 2.5 Consensus size: 65
358780 AATTAAATTG
* * * *
358790 AACATCGAATGCATTTCATGCATCAATGCA-CATACCATTCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATATTT-TG
358853 A
65 A
* * * *
358854 ATACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTTTG
1 A-ACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATATTTTG
358918 A
65 A
* *
358919 AACATTGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
358950 TCTTAGTGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
64 29 0.35
65 49 0.59
66 5 0.06
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:358949 original size:17 final size:19
Alignment explanation
Indices: 358927--358969 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
358917 GAAACATTGA
*
358927 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
358944 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
358963 ATGCACT
1 ATGCACT
358970 ATGGGTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:358965 original size:64 final size:63
Alignment explanation
Indices: 358791--358969 Score: 157
Period size: 65 Copynumber: 2.8 Consensus size: 63
358781 ATTAAATTGA
* * * * * * *
358791 ACATCGAATGCATTTCATGCATCAATGCACATACCATTCACCGATGCACTGAGGATTTTATGAAT
1 ACATCGAATGCACTTGATGCATCGATGCAC-CAGC-TGCACCGATGCACTCAGGATTTTATGAAT
* * * *
358856 ACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTT-TGAA
1 ACATCGAATGCACTTGATGCATCGATGCACCAG-C-TGCACCGATGCACTCAGGAT-TTTATGAA
358920 -
63 T
*
358920 ACATTGAATGCACTTGATGCATCGATGCACTCTTAG-TGCACCGATGCACT
1 ACATCGAATGCACTTGATGCATCGATGCAC-C--AGCTGCACCGATGCACT
358970 ATGGGTCCAA
Statistics
Matches: 97, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
64 42 0.43
65 50 0.52
66 3 0.03
67 2 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (63 bp):
ACATCGAATGCACTTGATGCATCGATGCACCAGCTGCACCGATGCACTCAGGATTTTATGAAT
Done.