Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008484.1 Hibiscus syriacus cultivar Beakdansim tig00111318_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: 688492
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:126995 original size:16 final size:16
Alignment explanation
Indices: 126857--127003 Score: 111
Period size: 16 Copynumber: 8.7 Consensus size: 16
126847 CTCATCCAGC
126857 AAAGAAAGAAGAAGGAAA
1 AAAGAAA-AA-AAGGAAA
*
126875 AAAAAAGAAAAAGGAAA
1 AAAGAA-AAAAAGGAAA
* *
126892 AAA-ACAAAAA-TAAA
1 AAAGAAAAAAAGGAAA
* *
126906 AAACAAAACAAA-AAAGA
1 AAAGAAAA-AAAGGAA-A
126923 AAAGGAAAAGGAAAAGGAAAA
1 AAA-G-AAA--AAAAGG-AAA
*
126944 AAAGAAAAAAAGAAAA
1 AAAGAAAAAAAGGAAA
126960 AAAGAAAAAAAGGAAA
1 AAAGAAAAAAAGGAAA
*
126976 AAAGGAAAAAAGGAAA
1 AAAGAAAAAAAGGAAA
126992 AAAGGAAAAAAA
1 AAA-GAAAAAAA
127004 AATTGAATCA
Statistics
Matches: 107, Mismatches: 11, Indels: 23
0.76 0.08 0.16
Matches are distributed among these distances:
14 6 0.06
15 8 0.07
16 42 0.39
17 26 0.24
18 7 0.07
19 7 0.07
20 4 0.04
21 5 0.05
22 2 0.02
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.01
Consensus pattern (16 bp):
AAAGAAAAAAAGGAAA
Found at i:129457 original size:114 final size:114
Alignment explanation
Indices: 129254--129479 Score: 373
Period size: 114 Copynumber: 2.0 Consensus size: 114
129244 AAGTGCCACG
*
129254 TTCTCGTAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* * *
129319 TGGTTTGGTATGAACCCTAAAACCAATCATTGGATTTGAAAAATGAATT
66 TGGTTCGGTATGAACCCCAAAACCAATCATTGGAATTGAAAAATGAATT
*
129368 TTCTCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
1 TTCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
* *
129433 TGGTTCGGTA-GAAACCCCAGAACCAATCATTGGAATTGAAAGATGAA
66 TGGTTCGGTATG-AACCCCAAAACCAATCATTGGAATTGAAAAATGAA
129480 CTGCATAATC
Statistics
Matches: 104, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
113 1 0.01
114 103 0.99
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (114 bp):
TTCTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC
TGGTTCGGTATGAACCCCAAAACCAATCATTGGAATTGAAAAATGAATT
Found at i:130439 original size:35 final size:35
Alignment explanation
Indices: 130388--130454 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
130378 TTCAAACAGA
130388 AATAGAATATTGGGGCATT-TT-GAAGGCTCATAAT
1 AATAGAATATTGGGGCATTCTTAG-AGGCTCATAAT
*
130422 AATATGAATATTTGGGCATTCTTAGAGGCTCAT
1 AATA-GAATATTGGGGCATTCTTAGAGGCTCAT
130455 CTCAACAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 4 0.14
35 14 0.48
36 10 0.34
37 1 0.03
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.34
Consensus pattern (35 bp):
AATAGAATATTGGGGCATTCTTAGAGGCTCATAAT
Found at i:131581 original size:54 final size:54
Alignment explanation
Indices: 131518--131679 Score: 263
Period size: 54 Copynumber: 3.0 Consensus size: 54
131508 TGATTGAGAA
* *
131518 ATCTTGGCAGAAGACACAGAAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTTGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
131572 ATCTTGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTTGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
* * *
131626 ATC-TGAGCAGAATCCACAGGAAAGGATGAATGCGCTGTCAAATGTTTTACGAAC
1 ATCTTG-GCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
131680 CTGCTATTCT
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
53 2 0.02
54 100 0.98
ACGTcount: A:0.35, C:0.15, G:0.25, T:0.25
Consensus pattern (54 bp):
ATCTTGGCAGAAGCCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:132062 original size:22 final size:22
Alignment explanation
Indices: 132031--132085 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
132021 ATCTACACTC
*
132031 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
132053 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
132075 TTCAAAGATGA
1 TTCAAAGATGA
132086 AAGCTTTATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.36
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:132683 original size:113 final size:113
Alignment explanation
Indices: 132484--132808 Score: 447
Period size: 113 Copynumber: 2.9 Consensus size: 113
132474 TTAGCAAAGA
*
132484 TTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTG
1 TTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* *
132549 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-
66 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTG
* * * *
132596 TCTCAAATCCATCACTCGATAGATCAGCTTTTCCAGAGATAGTTCATAATGAGAAGAACTCATCT
1 T-TCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCT
*
132661 GAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTG
65 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTG
** * * * * * * *
132710 TTTGAATTCATCATTTGATGGATCAAC-ATCCCTAGTGAAAGAGTTCATAATGAGAAAAACTCAT
1 TTCAAATCCATCACTTGATGGATCAGCTTTTCC-A--GAAAAAGTTCATAATGAGAAGAACTCAT
132774 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
63 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAA
132809 CTCATCTGAA
Statistics
Matches: 187, Mismatches: 21, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
112 4 0.02
113 123 0.66
114 1 0.01
115 59 0.32
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (113 bp):
TTCAAATCCATCACTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTG
Found at i:132811 original size:40 final size:40
Alignment explanation
Indices: 132747--132848 Score: 179
Period size: 40 Copynumber: 2.6 Consensus size: 40
132737 ATCCCTAGTG
*
132747 AAAG-AGTTCATAATGAGAAAAACTCATCTGAAGAAGGAA
1 AAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
*
132786 GAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 AAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
132826 AAAGAAGTTCATAATGAGAAGAA
1 AAAGAAGTTCATAATGAGAAGAA
132849 TTTGTTCAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
39 3 0.05
40 56 0.95
ACGTcount: A:0.51, C:0.09, G:0.23, T:0.18
Consensus pattern (40 bp):
AAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
Found at i:132821 original size:155 final size:153
Alignment explanation
Indices: 132636--132961 Score: 494
Period size: 155 Copynumber: 2.1 Consensus size: 153
132626 TTCCAGAGAT
*
132636 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAAAAGAAGTTCATAATGAGAAGAATTTATTC
* *
132701 AACCTTTT-GTTTGAATTCATCATTTGATGGATCAACA-TCCCTAGTGAAAGAGTTCATAATGAG
66 AA-CTTTTCGCTTGAATTCATCATTCGATGGATCAACATTCCC-AG-G-AAGAGTTCATAATGAG
* *
132764 AAAAACTCATCTGAAGAAGGAAGAAGA
127 AAAAACTCATCTGAAGAAAGAAAAAGA
* *
132791 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAAAAGAAGTTCATAATGAGAAGAATTTATTC
* * ** *
132856 AACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAATGAGAAGA
66 AACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTCCCAGGAAGAGTTCATAATGAGAAAA
132921 ACTCATCTGAAGAAAGAAAAAGA
131 ACTCATCTGAAGAAAGAAAAAGA
132944 AGTTCATAATGAGAAGAA
1 AGTTCATAATGAGAAGAA
132962 TTTGTTCAAC
Statistics
Matches: 157, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
153 56 0.36
154 6 0.04
155 92 0.59
156 3 0.02
ACGTcount: A:0.41, C:0.13, G:0.21, T:0.25
Consensus pattern (153 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAAAAGAAGTTCATAATGAGAAGAATTTATTC
AACTTTTCGCTTGAATTCATCATTCGATGGATCAACATTCCCAGGAAGAGTTCATAATGAGAAAA
ACTCATCTGAAGAAAGAAAAAGA
Found at i:132989 original size:113 final size:113
Alignment explanation
Indices: 132791--133089 Score: 490
Period size: 113 Copynumber: 2.6 Consensus size: 113
132781 AGGAAGAAGA
132791 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * *
132856 AACTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGGCG
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACATTGCCAGAGAG
*
132904 AGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
* * *
132969 AACTTTTTGCTCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAG
66 AACTTTTCGCTCGAATTCATCACTCGATGGATCAACATTGCCAGAGAG
* *
133017 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
133082 AATCTTTT
66 AA-CTTTT
133090 GCATGATTCT
Statistics
Matches: 173, Mismatches: 12, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
113 168 0.97
114 5 0.03
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAATTTGTTC
AACTTTTCGCTCGAATTCATCACTCGATGGATCAACATTGCCAGAGAG
Found at i:133000 original size:268 final size:266
Alignment explanation
Indices: 132517--133076 Score: 836
Period size: 268 Copynumber: 2.1 Consensus size: 266
132507 CAGCTTTTCC
* * *
132517 AGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAAT
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAATTCATAATGAGAAGAAT
* * * *
132582 TTGTTCAACCTTTTTCTCAAATCCATCACTCGATAGATCAGCTTTTCCAGAGATAGTTCATAATG
66 TTGTTCAACCTTTTGCTCAAATCCATCACTCGATAGATCAGCATTGCCAGAGAGAGTTCATAATG
* *
132647 AGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGTT
131 AGAAGAACTCATCTGAAGAAAGAAAAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCT
* * *
132712 TGAATTCATCATTTGATGGATCAAC-ATCCCTAGTGAAAGAGTTCATAATGAGAAAAACTCATCT
196 CGAATTCATCACTCGATGGATCAACTATCCC-A--GAAAGAGTTCATAATGAGAAAAACTCATCT
132776 GAAGAAGGA
258 GAAGAAGGA
*
132785 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAGTTCATAATGAGAAGAAT
1 AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAATTCATAATGAGAAGAAT
** * * * * *
132850 TTGTTCAA-CTTTTCGCTTGAATTCATCATTCGATGGATCAGCATTGCCAGGGCGAGTTCATAAT
66 TTGTTCAACCTTTT-GCTCAAATCCATCACTCGATAGATCAGCATTGCCAGAGAGAGTTCATAAT
* *
132914 GAGAAGAACTCATCTGAAGAAAGAAAAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGC
130 GAGAAGAACTCATCTGAAGAAAGAAAAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGC
* * * *
132979 TCGAATTCATCACTCGATGGATCAACTTTTCCAGAGAGAGTTCATAATGAGAAGAACTCATCTGA
195 TCGAATTCATCACTCGATGGATCAACTATCCCAGAAAGAGTTCATAATGAGAAAAACTCATCTGA
133044 AGAAGGA
260 AGAAGGA
133051 AGAAGAAGTTCATAATGAGAAGAACT
1 AGAAGAAGTTCATAATGAGAAGAACT
133077 TGTTCAATCT
Statistics
Matches: 264, Mismatches: 26, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
266 63 0.24
267 5 0.02
268 193 0.73
269 3 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (266 bp):
AGAAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAAAAGAAATTCATAATGAGAAGAAT
TTGTTCAACCTTTTGCTCAAATCCATCACTCGATAGATCAGCATTGCCAGAGAGAGTTCATAATG
AGAAGAACTCATCTGAAGAAAGAAAAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTGCT
CGAATTCATCACTCGATGGATCAACTATCCCAGAAAGAGTTCATAATGAGAAAAACTCATCTGAA
GAAGGA
Found at i:133357 original size:3 final size:3
Alignment explanation
Indices: 133351--133427 Score: 81
Period size: 3 Copynumber: 25.7 Consensus size: 3
133341 TTTATTTGAA
*
133351 TAT TAT T-T ATAT TAT TAT TAT TA- TAT ATAT ATAT TAT TAT TAT CAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT -TAT -TAT TAT TAT TAT TAT
133397 TA- TAT ATAT TAT TA- TAT TAT TAT TAT TAT TA
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TA
133428 AAAAAATAAT
Statistics
Matches: 65, Mismatches: 2, Indels: 14
0.80 0.02 0.17
Matches are distributed among these distances:
2 7 0.11
3 47 0.72
4 11 0.17
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:133439 original size:29 final size:29
Alignment explanation
Indices: 133380--133439 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
133370 ATTATATATA
* * * *
133380 TATATTATTATTATCATTATATATATTAT
1 TATATTATTATTATCATTAAAAAAATAAT
*
133409 TATATTATTATTATTATTAAAAAAATAAT
1 TATATTATTATTATCATTAAAAAAATAAT
133438 TA
1 TA
133440 CAAGCCCAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
TATATTATTATTATCATTAAAAAAATAAT
Found at i:134988 original size:20 final size:19
Alignment explanation
Indices: 134963--135002 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
134953 TTATTTTATA
134963 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
134983 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
135002 A
1 A
135003 TATCAGGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:135000 original size:119 final size:118
Alignment explanation
Indices: 134858--135095 Score: 293
Period size: 119 Copynumber: 2.0 Consensus size: 118
134848 TATTTTAATC
* * * *
134858 TTGTTTTAATATTTATTTATTTTTCAATATTA-AGAAATG-GCAGTCTTAAAACAACTGGATGTC
1 TTGTTTTAATATTTATTTATTTTT-AATATCAGAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-
* *
134921 CATTTTCTAATATTTTTAAATAAATAAATATCTTATTTTATAAAT-TATATATTAA
64 CATTTTCTAATATTTCTAAATAAATAAATATCTTA-TTTATAAATATATAAATTAA
* * * ** *
134976 TTGTTTTAATTATTTATTTATTTTTTATATCAGGGAAAAGAGCTGTCTTAAGGCACCTAGAAGTC
1 TTGTTTTAA-TATTTATTTATTTTTAATATCAGAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* *
135041 ATTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAA
65 ATTTTCTAATATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAA
135095 T
1 T
135096 ATATATTTTT
Statistics
Matches: 102, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
118 23 0.23
119 62 0.61
120 17 0.17
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (118 bp):
TTGTTTTAATATTTATTTATTTTTAATATCAGAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTAATATTTCTAAATAAATAAATATCTTATTTATAAATATATAAATTAA
Found at i:158576 original size:23 final size:22
Alignment explanation
Indices: 158549--158595 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
158539 AACCCTAAAT
158549 AAGCCCAAAAACCGTATCTGCTA
1 AAGCCC-AAAACCGTATCTGCTA
* * *
158572 AAGCCCAGAATCGTATCTTCTA
1 AAGCCCAAAACCGTATCTGCTA
158594 AA
1 AA
158596 CTCGAGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.38, C:0.28, G:0.13, T:0.21
Consensus pattern (22 bp):
AAGCCCAAAACCGTATCTGCTA
Found at i:165494 original size:38 final size:38
Alignment explanation
Indices: 165443--165515 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
165433 CCTTCTCCTG
* * *
165443 CAATTTGTATTCTTCGGTTGATTTTTTGGGTTTGTATT
1 CAATTTGTATTCTTCGATTGATTGTTTGGGGTTGTATT
*
165481 CAATTTGTTTTCTTCGATTGATTGTTTGGGGTTGT
1 CAATTTGTATTCTTCGATTGATTGTTTGGGGTTGT
165516 TGCTTTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.12, C:0.08, G:0.23, T:0.56
Consensus pattern (38 bp):
CAATTTGTATTCTTCGATTGATTGTTTGGGGTTGTATT
Found at i:167509 original size:6 final size:6
Alignment explanation
Indices: 167494--167530 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
167484 GCTTAAATAT
167494 ATGC-A ATGCAA ATGCAA ATGCTAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGCAA ATGC-AA ATGCAA ATGCAA A
167531 AAGGTGTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
7 6 0.20
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATGCAA
Found at i:167521 original size:13 final size:12
Alignment explanation
Indices: 167494--167530 Score: 58
Period size: 13 Copynumber: 3.1 Consensus size: 12
167484 GCTTAAATAT
167494 ATGC-AATGCAA
1 ATGCAAATGCAA
167505 ATGCAAATGCTAA
1 ATGCAAATGC-AA
167518 ATGCAAATGCAA
1 ATGCAAATGCAA
167530 A
1 A
167531 AAGGTGTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 4 0.17
12 8 0.33
13 12 0.50
ACGTcount: A:0.49, C:0.16, G:0.16, T:0.19
Consensus pattern (12 bp):
ATGCAAATGCAA
Found at i:173742 original size:15 final size:15
Alignment explanation
Indices: 173715--173747 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
173705 TAATAATTAT
173715 AATAATAAAAATAAA
1 AATAATAAAAATAAA
173730 AATAA-AAACAATAAA
1 AATAATAAA-AATAAA
173745 AAT
1 AAT
173748 CCCGAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.79, C:0.03, G:0.00, T:0.18
Consensus pattern (15 bp):
AATAATAAAAATAAA
Found at i:175754 original size:25 final size:26
Alignment explanation
Indices: 175719--175768 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
175709 AATTTTTTTT
*
175719 TAAAAATATT-ATATA-ATTATAAAAA
1 TAAAAAAATTAATATACATTA-AAAAA
175744 TAAAAAAATTAATATACATTAAAAA
1 TAAAAAAATTAATATACATTAAAAA
175769 TTTCACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 9 0.41
26 9 0.41
27 4 0.18
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (26 bp):
TAAAAAAATTAATATACATTAAAAAA
Found at i:183675 original size:25 final size:26
Alignment explanation
Indices: 183628--183676 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
183618 TAAAATTAAG
*
183628 ATTTATATAAAAAGATAACCTATAAC
1 ATTTATATAAAAAGATAAACTATAAC
* *
183654 ATTTAT-TAAAAGGGTAAACTATA
1 ATTTATATAAAAAGATAAACTATA
183677 CCAATGACCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 14 0.70
26 6 0.30
ACGTcount: A:0.51, C:0.08, G:0.08, T:0.33
Consensus pattern (26 bp):
ATTTATATAAAAAGATAAACTATAAC
Found at i:184752 original size:60 final size:60
Alignment explanation
Indices: 184685--184811 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
184675 ACAAATGATT
* * *
184685 CTGACTATAGGATATTACTTTGTTGAGTTCTAT-AATTATTAAAAATTATAAAATGGTCCC
1 CTGACTATAGGATATTACTTTGTTGAGTT-TATCAACTATTAAAAATTACAAAATGGTCAC
* * * * * *
184745 CTGACTATAGGGTGTTATTTTGTTGTGTTTATCGACTATTAAAAGTTACAAAATGGTCAC
1 CTGACTATAGGATATTACTTTGTTGAGTTTATCAACTATTAAAAATTACAAAATGGTCAC
184805 C-GACTAT
1 CTGACTAT
184812 TCATTATACT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 9 0.16
60 48 0.84
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (60 bp):
CTGACTATAGGATATTACTTTGTTGAGTTTATCAACTATTAAAAATTACAAAATGGTCAC
Found at i:186841 original size:64 final size:66
Alignment explanation
Indices: 186736--186898 Score: 206
Period size: 65 Copynumber: 2.5 Consensus size: 66
186726 CGGTTCACCA
* *
186736 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTG-GTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCAATGCATG
186799 G
66 G
** * **
186800 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCAATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCAATGCATG
186864 G
66 G
* * * *
186865 AGAGTGTATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
186899 CAATTAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 37 0.45
65 46 0.55
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (66 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCAATGCATG
G
Found at i:186870 original size:19 final size:19
Alignment explanation
Indices: 186846--186884 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
186836 GAAAATATTC
186846 AGAGTGCATCAATGCATGG
1 AGAGTGCATCAATGCATGG
* **
186865 AGAGTGTATCGGTGCATGG
1 AGAGTGCATCAATGCATGG
186884 A
1 A
186885 ATGCATTCGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.36, T:0.23
Consensus pattern (19 bp):
AGAGTGCATCAATGCATGG
Found at i:186941 original size:65 final size:65
Alignment explanation
Indices: 186740--186946 Score: 178
Period size: 65 Copynumber: 3.2 Consensus size: 65
186730 TCACCAAGTG
* * * ** *
186740 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATCAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
186803 G-
64 GA
* * *
186804 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCAATGCATGGA--G
1 TGCATCGGTGCATCAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
186867 A
65 A
* ** *
186868 GTGTATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
186930 CTGA
62 CTGA
186934 TGCATCGGTGCAT
1 TGCATCGGTGCAT
186947 TACTTTGAAT
Statistics
Matches: 119, Mismatches: 14, Indels: 19
0.78 0.09 0.12
Matches are distributed among these distances:
62 3 0.03
63 8 0.07
64 50 0.42
65 56 0.47
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:187330 original size:28 final size:30
Alignment explanation
Indices: 187273--187331 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
187263 ATTGATTTTG
*
187273 AAAAACTTACTCCCCCTTACTATAGCACATC
1 AAAAACTTACT-CCCCTTACTATAACACATC
187304 AAAAACTTACT-CCC-TACTATAACACATC
1 AAAAACTTACTCCCCTTACTATAACACATC
187332 TTAAATTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 13 0.48
29 3 0.11
31 11 0.41
ACGTcount: A:0.39, C:0.34, G:0.02, T:0.25
Consensus pattern (30 bp):
AAAAACTTACTCCCCTTACTATAACACATC
Found at i:195442 original size:64 final size:66
Alignment explanation
Indices: 195337--195499 Score: 224
Period size: 65 Copynumber: 2.5 Consensus size: 66
195327 CGGTGCACCA
*
195337 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATAGCCTG-GTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
195400 G
66 G
** * **
195401 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAGAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
195465 G
66 G
* * *
195466 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
195500 CAATTAATTC
Statistics
Matches: 85, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
64 37 0.44
65 48 0.56
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (66 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATAGCCAGAGTGCATCGATGCATG
G
Found at i:195471 original size:19 final size:19
Alignment explanation
Indices: 195447--195497 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
195437 GAAAATATTC
195447 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
195466 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
195485 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
195498 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:195539 original size:65 final size:65
Alignment explanation
Indices: 195341--195547 Score: 187
Period size: 65 Copynumber: 3.2 Consensus size: 65
195331 GCACCAAGTG
* * * ** *
195341 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG-CTT
1 TGCATCGGTGCATCAAATGCATTCGATGTTT-CAAAATATTCAGAGTGCATCGATGCATGGAC-T
195404 G-
64 GA
* *
195405 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGGA--G
1 TGCATCGGTGCATCAAATGCATTCGATG-TTTCAAAATATTCAGAGTGCATCGATGCATGGACTG
195468 A
65 A
** *
195469 GTGCATCGGTGCATGGAATGCATTCGATG-TTC-AATTAATTCATCGA-TGCATCGATGCATGGA
1 -TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAAT-ATTCA--GAGTGCATCGATGCATGGA
195531 CTGA
62 CTGA
*
195535 TGCATCAGTGCAT
1 TGCATCGGTGCAT
195548 TACTTTGAAT
Statistics
Matches: 122, Mismatches: 11, Indels: 19
0.80 0.07 0.12
Matches are distributed among these distances:
62 3 0.02
63 8 0.07
64 51 0.42
65 58 0.48
66 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (65 bp):
TGCATCGGTGCATCAAATGCATTCGATGTTTCAAAATATTCAGAGTGCATCGATGCATGGACTGA
Found at i:197019 original size:22 final size:22
Alignment explanation
Indices: 196970--197020 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
196960 TCTATGCTAT
* *
196970 TAAAAAATTGAATTCATAAATG
1 TAAAAAATTAAATTCATAAATA
*
196992 TAAAAAATTAAATTC-TAACTA
1 TAAAAAATTAAATTCATAAATA
197013 TATAAAAA
1 TA-AAAAA
197021 CTTTATTAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 6 0.24
22 19 0.76
ACGTcount: A:0.59, C:0.06, G:0.04, T:0.31
Consensus pattern (22 bp):
TAAAAAATTAAATTCATAAATA
Found at i:197751 original size:21 final size:21
Alignment explanation
Indices: 197727--197782 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
197717 CGAAAATATT
*
197727 TATTTTAGATAACAAAATTAA
1 TATTTTAGATAACAAAAATAA
* *
197748 TATTTTCGATAAAAAAAATAA
1 TATTTTAGATAACAAAAATAA
* *
197769 CATTTTAAATAACA
1 TATTTTAGATAACA
197783 CTTTACTAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.36
Consensus pattern (21 bp):
TATTTTAGATAACAAAAATAA
Found at i:200148 original size:25 final size:25
Alignment explanation
Indices: 200120--200169 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
200110 ACATCATCCT
*
200120 TATGATCATGCAATCACTATTTTAA
1 TATGATCATGCAATAACTATTTTAA
200145 TATGATCATGCAATAACTATTTTAA
1 TATGATCATGCAATAACTATTTTAA
200170 ACAGTCTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (25 bp):
TATGATCATGCAATAACTATTTTAA
Found at i:216350 original size:263 final size:266
Alignment explanation
Indices: 215883--216409 Score: 1033
Period size: 263 Copynumber: 2.0 Consensus size: 266
215873 GTGTCCATTG
215883 CTCCCTATCGCATGGCACCAACTGAGCTAAAGGAGCTGAAGGCTCAGATTCAAGAGTTGCTAGAG
1 CTCCCTATCGCATGGCACCAACTGAGCTAAAGGAGCTGAAGGCTCAGATTCAAGAGTTGCTAGAG
215948 AAATGTTTCATTCAATCGAGTATATCTCCTTGTGGAGTACCTGTCTTATTCGTTAAGAAGAAAAA
66 AAATGTTTCATTCAATCGAGTATATCTCCTTGTGGAGTACCTGTCTTATTCGTTAAGAAGAAAAA
216013 TGGGTCGATGAGGTTGTGCATCGACTATAGGCAGTTAAATAAGTTGATCATCAAGAATTGTTACC
131 TGGGTCGATGAGGTTGTGCATCGACTATAGGCAGTTAAATAAGTTGATCATCAAGAATTGTTACC
216078 TACTCCCCAAGATAGATTACCTCTTCAACCAGCTCAG-GGGGCATG-GTCTTCCC-AAGATTGAT
196 TACTCCCCAAGATAGATTACCTCTTCAACCAGCTCAGAGGGGCATGTGTCTTCCCAAAGATTGAT
216140 ATGCTT
261 ATGCTT
216146 CTCCCTATCGCATGGCACCAACTGAGCTAAAGGAGCTGAAGGCTCAGATTCAAGAGTTGCTAGAG
1 CTCCCTATCGCATGGCACCAACTGAGCTAAAGGAGCTGAAGGCTCAGATTCAAGAGTTGCTAGAG
216211 AAATGTTTCATTCAATCGAGTATATCTCCTTGTGGAGTACCTGTCTTATTCGTTAAGAAGAAAAA
66 AAATGTTTCATTCAATCGAGTATATCTCCTTGTGGAGTACCTGTCTTATTCGTTAAGAAGAAAAA
216276 TGGGTCGATGAGGTTGTGCATCGACTATAGGCAGTTAAATAAGTTGATCATCAAGAATTGTTACC
131 TGGGTCGATGAGGTTGTGCATCGACTATAGGCAGTTAAATAAGTTGATCATCAAGAATTGTTACC
216341 TACTCCCCAAGATAGATTACCTCTTCAACCAGCTCAGAGGGGCATGTGTCTTCCCAAAGATTGAT
196 TACTCCCCAAGATAGATTACCTCTTCAACCAGCTCAGAGGGGCATGTGTCTTCCCAAAGATTGAT
216406 ATGC
261 ATGC
216410 GATTAGGCTA
Statistics
Matches: 261, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
263 232 0.89
264 8 0.03
265 8 0.03
266 13 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.28
Consensus pattern (266 bp):
CTCCCTATCGCATGGCACCAACTGAGCTAAAGGAGCTGAAGGCTCAGATTCAAGAGTTGCTAGAG
AAATGTTTCATTCAATCGAGTATATCTCCTTGTGGAGTACCTGTCTTATTCGTTAAGAAGAAAAA
TGGGTCGATGAGGTTGTGCATCGACTATAGGCAGTTAAATAAGTTGATCATCAAGAATTGTTACC
TACTCCCCAAGATAGATTACCTCTTCAACCAGCTCAGAGGGGCATGTGTCTTCCCAAAGATTGAT
ATGCTT
Found at i:226019 original size:21 final size:21
Alignment explanation
Indices: 225981--226062 Score: 53
Period size: 21 Copynumber: 3.8 Consensus size: 21
225971 CAGAACCCCA
* *
225981 GGGGGGTATCGATCCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
226002 GGGGGGAATCGGTTCCCCT-T
1 GGGGGGAATCGATTCCCCTGT
* *
226022 CAAAGGGGGAATCGGTTCCCTCATG-
1 ---GGGGGGAATCGATTCCC-C-TGT
226047 GGGGGG-ATCGATTCCC
1 GGGGGGAATCGATTCCC
226063 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
20 1 0.02
21 25 0.51
22 5 0.10
23 16 0.33
24 1 0.02
25 1 0.02
ACGTcount: A:0.15, C:0.26, G:0.38, T:0.22
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:229561 original size:22 final size:22
Alignment explanation
Indices: 229520--229587 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
229510 CTCGTATAAA
229520 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
229543 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
229565 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
229587 T
1 T
229588 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:230312 original size:66 final size:64
Alignment explanation
Indices: 230211--230364 Score: 209
Period size: 66 Copynumber: 2.3 Consensus size: 64
230201 ATCGGTTCCC
* *
230211 CCCCCTGGGGGTATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGATGAGGGGGTATCGGT
1 CCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCAT-T-CGATGAGGGGGTATCGGT
230276 T
64 T
* * *
230277 CCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCATTCGTTGAGGGGGTATCGGTT
1 CCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTCGATGAGGGGGTATCGGTT
* *
230341 CCCCTTGAATGGGTACCGATTCCC
1 CCCCCTG--GGGGTACCGATTCCC
230365 TTAACCCAGA
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
64 24 0.30
65 1 0.01
66 54 0.68
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (64 bp):
CCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATTCGATGAGGGGGTATCGGTT
Found at i:236239 original size:22 final size:22
Alignment explanation
Indices: 236198--236265 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
236188 CTCGTATAAA
236198 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
236221 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
236243 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
236265 T
1 T
236266 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 33 0.73
23 12 0.27
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:237044 original size:67 final size:67
Alignment explanation
Indices: 236874--237024 Score: 214
Period size: 67 Copynumber: 2.3 Consensus size: 67
236864 TTTTTCTCAT
* * * *
236874 GGGGGAATCGGTTCCCCCCCTGGGGATATCGATTCCCCTCAAGCAATCTGGAATTTCATATACGA
1 GGGGGTATCGGTT-CCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGA
236939 TGA
65 TGA
* * * *
236942 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCTAGCATTCTGGAAATTCAT-TTCGTT
1 GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
237006 GA
66 GA
237008 GGGGGTATCGGTTCCCC
1 GGGGGTATCGGTTCCCC
237025 TTGAATGGGT
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
66 23 0.31
67 40 0.53
68 12 0.16
ACGTcount: A:0.18, C:0.27, G:0.28, T:0.27
Consensus pattern (67 bp):
GGGGGTATCGGTTCCCCCCTGGGGGTACCGATTCCCCTCAAGCAATCTGGAAATTCATATACGAT
GA
Found at i:244002 original size:21 final size:22
Alignment explanation
Indices: 243936--244008 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 22
243926 GTGCAGAGGT
*
243936 AATCGATACCCT-CTTGAAGAGG
1 AATCGATTCCCTCCTTGAAG-GG
243958 AATCGATTCCC-CCTTTGAATGGG
1 AATCGATTCCCTCC-TTGAA-GGG
*
243981 AACCGATTCCCTCCTTG-AGGG
1 AATCGATTCCCTCCTTGAAGGG
244002 AATCGAT
1 AATCGAT
244009 ACCCCCCATG
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
21 9 0.20
22 12 0.27
23 20 0.45
24 3 0.07
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.26
Consensus pattern (22 bp):
AATCGATTCCCTCCTTGAAGGG
Found at i:249543 original size:20 final size:20
Alignment explanation
Indices: 249520--249557 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
249510 TGTCTTGTTT
249520 TTCAAAT-TGTTGTGTTTTGA
1 TTCAAATATGTTGT-TTTTGA
*
249540 TTCAATTATGTTGTTTTT
1 TTCAAATATGTTGTTTTT
249558 CATGAAAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (20 bp):
TTCAAATATGTTGTTTTTGA
Found at i:268649 original size:22 final size:22
Alignment explanation
Indices: 268621--268662 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
268611 GGCGACATCC
*
268621 GTCCCCATCTCTGACGAAATAT
1 GTCCCCATCTCCGACGAAATAT
268643 GTCCCCATCTCCGACGAAAT
1 GTCCCCATCTCCGACGAAAT
268663 TCGTCTATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.26, C:0.36, G:0.14, T:0.24
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATAT
Found at i:270788 original size:21 final size:21
Alignment explanation
Indices: 270764--270854 Score: 112
Period size: 21 Copynumber: 4.3 Consensus size: 21
270754 CCTGTTATCG
*
270764 TTCAAGAGGCCCCTATCATCC
1 TTCAAGAGGCCCCTCTCATCC
*
270785 TTCAAGAGGCCCCTCCCA-CC
1 TTCAAGAGGCCCCTCTCATCC
* *
270805 GTTCAAGAGGCCCCTGTCATCG
1 -TTCAAGAGGCCCCTCTCATCC
* *
270827 TTCAAGAGGTCCCTCTCATCA
1 TTCAAGAGGCCCCTCTCATCC
270848 TTCAAGA
1 TTCAAGA
270855 ACCCGATTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
20 2 0.03
21 57 0.95
22 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCTCATCC
Found at i:270809 original size:42 final size:42
Alignment explanation
Indices: 270762--270841 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 42
270752 CACCTGTTAT
270762 CGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCAC
* * *
270804 CGTTCAAGAGGCCCCTGTCATCGTTCAAGAGGTCCCTC
1 CGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTC
270842 TCATCATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCAC
Found at i:270852 original size:42 final size:42
Alignment explanation
Indices: 270764--270854 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
270754 CCTGTTATCG
*
270764 TTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACCG
1 TTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACCA
* * * * *
270806 TTCAAGAGGCCCCTGTCATCGTTCAAGAGGTCCCTCTCATCA
1 TTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACCA
270848 TTCAAGA
1 TTCAAGA
270855 ACCCGATTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCCTTCAAGAGGCCCCTCCCACCA
Found at i:272276 original size:64 final size:64
Alignment explanation
Indices: 272203--272351 Score: 244
Period size: 64 Copynumber: 2.3 Consensus size: 64
272193 AAATTGATGT
272203 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
* * ***
272267 ATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAATTG
1 ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
*
272331 ATTTGTAAATGTTGATTTGTT
1 ATTTGTAAAAGTTGATTTGTT
272352 GTTTTAAATT
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
64 79 1.00
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (64 bp):
ATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAAAATTATTTTTTGCTTGTTTAATTG
Found at i:272441 original size:20 final size:20
Alignment explanation
Indices: 272410--272493 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
272400 AAGCTACACT
*
272410 TTCGCAACGCGAAAGTCAAA
1 TTCGTAACGCGAAAGTCAAA
*** *
272430 TTCGTGTTGCGATAGTCAAA
1 TTCGTAACGCGAAAGTCAAA
*
272450 TTC-TCAACGCGAAAGCCAAA
1 TTCGT-AACGCGAAAGTCAAA
*
272470 TTCGTAACGCGAAAGTCAAC
1 TTCGTAACGCGAAAGTCAAA
272490 TTCG
1 TTCG
272494 CGTTGCGATT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 1 0.02
20 48 0.96
21 1 0.02
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (20 bp):
TTCGTAACGCGAAAGTCAAA
Found at i:272759 original size:6 final size:6
Alignment explanation
Indices: 272750--272784 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
272740 TTGTGATTGG
**
272750 GATTTT GATTTT GATTGC GATTTT GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
272785 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:272766 original size:18 final size:18
Alignment explanation
Indices: 272743--272783 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
272733 GAAGCCGTTG
*
272743 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
272761 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
272779 TGATT
1 TGATT
272784 TCCTTTTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:274859 original size:12 final size:12
Alignment explanation
Indices: 274843--274872 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
274833 TCTTCGGGGA
274843 CTTCTTTTTCTT
1 CTTCTTTTTCTT
*
274855 TTTCTTTTTCTT
1 CTTCTTTTTCTT
274867 CTTCTT
1 CTTCTT
274873 CAGGGTTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (12 bp):
CTTCTTTTTCTT
Found at i:276079 original size:20 final size:20
Alignment explanation
Indices: 276056--276156 Score: 73
Period size: 20 Copynumber: 5.0 Consensus size: 20
276046 TAAAATTCGT
276056 GTTGCGAATTCGAAAATCGA
1 GTTGCGAATTCGAAAATCGA
* * *
276076 GTTGCTACA-AC-AAAATTCGC
1 GTTGCGA-ATTCGAAAA-TCGA
276096 GTTGCGAATTC-AGAAATCGA
1 GTTGCGAATTCGA-AAATCGA
* * *
276116 GTTGCGAATTTGAAATTCAA
1 GTTGCGAATTCGAAAATCGA
*
276136 TGTTGCGAATTTGGAAAATCG
1 -GTTGCGAA-TTCGAAAATCG
276157 CAATGCGATT
Statistics
Matches: 62, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
19 5 0.08
20 36 0.58
21 13 0.21
22 8 0.13
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (20 bp):
GTTGCGAATTCGAAAATCGA
Found at i:276132 original size:40 final size:41
Alignment explanation
Indices: 276048--276227 Score: 122
Period size: 40 Copynumber: 4.4 Consensus size: 41
276038 TGCTAAATTA
* * ***
276048 AAATTCGTGTTGCGAATTC-GAAAATCGAGTTGCTACA-ACA
1 AAATTCGCGTTGCGAATTCGGAAAATCGAGTTGCGA-ATTTG
*
276088 AAATTCGCGTTGCGAATTCAG-AAATCGAGTTGCGAATTTG
1 AAATTCGCGTTGCGAATTCGGAAAATCGAGTTGCGAATTTG
** * *
276128 AAATTCAATGTTGCGAATTTGGAAAATCGCA-ATGCG-ATTT-
1 AAATTC-GCGTTGCGAATTCGGAAAATCG-AGTTGCGAATTTG
* * * *
276168 ACATATTCGCGTTGCGAATTTGGAAACT-GAGTTACGAAATTG
1 A-A-ATTCGCGTTGCGAATTCGGAAAATCGAGTTGCGAATTTG
* *
276210 GAGTTCGCGTTGCGAATT
1 AAATTCGCGTTGCGAATT
276228 TGTTGGTCAT
Statistics
Matches: 112, Mismatches: 18, Indels: 20
0.75 0.12 0.13
Matches are distributed among these distances:
39 2 0.02
40 57 0.51
41 38 0.34
42 14 0.12
43 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (41 bp):
AAATTCGCGTTGCGAATTCGGAAAATCGAGTTGCGAATTTG
Found at i:277835 original size:13 final size:13
Alignment explanation
Indices: 277817--277841 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
277807 TTCCAATGGC
277817 AGGATCATGCTAA
1 AGGATCATGCTAA
277830 AGGATCATGCTA
1 AGGATCATGCTA
277842 TATTACATGA
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:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (13 bp):
AGGATCATGCTAA
Found at i:278987 original size:2 final size:2
Alignment explanation
Indices: 278980--279023 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
278970 AACAAAAATA
278980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
279022 AT
1 AT
279024 TAACACTAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:282226 original size:29 final size:29
Alignment explanation
Indices: 282091--282230 Score: 106
Period size: 30 Copynumber: 4.8 Consensus size: 29
282081 TAGCAAGAAT
* *
282091 AAAACTCAAAGGACCAAAATAATATAAACA
1 AAAACTTAAAGGACTAAAATAA-ATAAACA
* * ** *
282121 AAAATTTAAAGGACTGAAATAGCTAAAAA
1 AAAACTTAAAGGACTAAAATAAATAAACA
* * * *
282150 AGAAACAT-AGGGACTTAAATAGATAAAACA
1 A-AAACTTAAAGGACTAAAATAAAT-AAACA
**
282180 AAAACTTAAAGGGTTAAAATATAATAAACA
1 AAAACTTAAAGGACTAAAATA-AATAAACA
282210 AAAA-TTAAAGGACT-AAATAAA
1 AAAACTTAAAGGACTAAAATAAA
282231 ATAGAAACTT
Statistics
Matches: 85, Mismatches: 21, Indels: 11
0.73 0.18 0.09
Matches are distributed among these distances:
27 2 0.02
28 5 0.06
29 32 0.38
30 44 0.52
31 2 0.02
ACGTcount: A:0.61, C:0.09, G:0.11, T:0.19
Consensus pattern (29 bp):
AAAACTTAAAGGACTAAAATAAATAAACA
Found at i:284018 original size:16 final size:16
Alignment explanation
Indices: 283997--284028 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
283987 TTACACCCTA
*
283997 AAATTTTTTATATTTT
1 AAATTTTTTAAATTTT
284013 AAATTTTTTAAATTTT
1 AAATTTTTTAAATTTT
284029 TTATTGATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AAATTTTTTAAATTTT
Found at i:292746 original size:20 final size:20
Alignment explanation
Indices: 292723--292772 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
292713 ACTCAATTTC
292723 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
292743 CAAATTCGCAACACAGAAGT
1 CAAATTCGCAACACAGAAGT
292763 CAAATTCGCA
1 CAAATTCGCA
292773 GAGCGCGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.44, C:0.26, G:0.14, T:0.16
Consensus pattern (20 bp):
CAAATTCGCAACACAGAAGT
Found at i:294794 original size:14 final size:14
Alignment explanation
Indices: 294775--294804 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
294765 TAATTTATTA
294775 GTAAAAGTTGATTT
1 GTAAAAGTTGATTT
294789 GTAAAAGTTGATTT
1 GTAAAAGTTGATTT
294803 GT
1 GT
294805 TTAATTGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.23, T:0.43
Consensus pattern (14 bp):
GTAAAAGTTGATTT
Found at i:294801 original size:78 final size:78
Alignment explanation
Indices: 294704--294868 Score: 249
Period size: 78 Copynumber: 2.1 Consensus size: 78
294694 GCTTGTTTAA
*
294704 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTGTTTTTTGCTCGTTTAAT
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTCGTTTAAT
*
294769 TTATTAGTAAAAG
66 TGATTAGTAAAAG
* * *** *
294782 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGTGTAAATAATTCTTATTTTTTGCTTGTTTAAT
1 TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTCGTTTAAT
*
294847 TGATTTGTAAAAG
66 TGATTAGTAAAAG
294860 TTGATTTGT
1 TTGATTTGT
294869 TGTTTTAAAT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.29, C:0.02, G:0.18, T:0.50
Consensus pattern (78 bp):
TTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGCTCGTTTAAT
TGATTAGTAAAAG
Found at i:295009 original size:29 final size:29
Alignment explanation
Indices: 294983--295057 Score: 107
Period size: 29 Copynumber: 2.6 Consensus size: 29
294973 ATTTCGCATT
294983 TCGAATTTGACTTTCGCAACAATCGCAAC
1 TCGAATTTGACTTTCGCAACAATCGCAAC
* * *
295012 GCGAATTTGACTTTCACAACAATTGCAAC
1 TCGAATTTGACTTTCGCAACAATCGCAAC
295041 GT-GAATTTGACTTTCGC
1 -TCGAATTTGACTTTCGC
295058 GTTGCGAATT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (29 bp):
TCGAATTTGACTTTCGCAACAATCGCAAC
Found at i:297553 original size:24 final size:24
Alignment explanation
Indices: 297519--297571 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
297509 ATGAAACATC
297519 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
297543 ATCAAAGTCCGGGTATTGGCCAAG
1 ATCAAAATCCGAGTATTGACCAAG
297567 ATCAA
1 ATCAA
297572 TTTTCGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:297719 original size:12 final size:12
Alignment explanation
Indices: 297698--297731 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
297688 GGTTGTGGGT
*
297698 TTTGAGATTGTG
1 TTTGATATTGTG
297710 TTTGATATTGTG
1 TTTGATATTGTG
*
297722 TTTGGTATTG
1 TTTGATATTG
297732 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:298362 original size:14 final size:15
Alignment explanation
Indices: 298326--298363 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
298316 GAAATCATTG
298326 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
298341 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
298356 AAAAATTA
1 AAAAATTA
298364 GAGATGGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:298608 original size:20 final size:20
Alignment explanation
Indices: 298539--298601 Score: 101
Period size: 20 Copynumber: 3.1 Consensus size: 20
298529 TAAAATTTGT
*
298539 GTTGCAAATTC-GAAAATCGA
1 GTTGCGAATTCAG-AAATCGA
298559 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATTCAGAAATCGA
298579 GTTGCGAATTCAGAAATCGA
1 GTTGCGAATTCAGAAATCGA
298599 GTT
1 GTT
298602 TTGAATTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 40 0.98
21 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (20 bp):
GTTGCGAATTCAGAAATCGA
Found at i:298645 original size:20 final size:20
Alignment explanation
Indices: 298552--298691 Score: 86
Period size: 20 Copynumber: 7.0 Consensus size: 20
298542 GCAAATTCGA
* **
298552 AAATCGAGTTGCGAATTCAG
1 AAATTGAGTTGCGAATTTGG
* **
298572 AAATCGAGTTGCGAATTCAG
1 AAATTGAGTTGCGAATTTGG
* **
298592 AAATCGAGTTTTGAATTT-G
1 AAATTGAGTTGCGAATTTGG
**
298611 AAATCCAATGTTGCGAATTTGG
1 AAAT-TGA-GTTGCGAATTTGG
*
298633 AAATTGCGTTGCGAATTTGG
1 AAATTGAGTTGCGAATTTGG
* * *
298653 AAACTGAGTTGTGAAATTGG
1 AAATTGAGTTGCGAATTTGG
* *
298673 -AGTTCGTGTTGCGAATTTG
1 AAATT-GAGTTGCGAATTTG
298692 TTGGTCATTT
Statistics
Matches: 98, Mismatches: 18, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
19 7 0.07
20 77 0.79
21 9 0.09
22 5 0.05
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (20 bp):
AAATTGAGTTGCGAATTTGG
Found at i:298947 original size:2 final size:2
Alignment explanation
Indices: 298940--298979 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
298930 ATCATAAAAT
298940 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
298980 AACTTTTAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:301317 original size:107 final size:104
Alignment explanation
Indices: 301130--301339 Score: 289
Period size: 107 Copynumber: 2.0 Consensus size: 104
301120 AAAAATCACA
* * *
301130 GCTGGAGAGAATGAAACGGTCTCACCAAAAACTAGAGGAGAACACCCAAAACGCGTAGCAGCTTT
1 GCTGGAGAGAAAGAAACGGACTCACCAAAAACTAGAGAAGAACACCCAAAACGCGTAGCAGCTTT
* *
301195 GGGGACGAAAGTCGAACGAAACCTAATCCCCAAAATCACCTG
66 GGGGACAAAAATCG-A--AAACCTAATCCCCAAAATCACCTG
* * *
301237 GCTGGAGAGAAAGAAAACGGACTCACC-AAAACTAGCA-AAGAACACCCAAATCTCGTAGCATCT
1 GCTGGAGAGAAAG-AAACGGACTCACCAAAAACTAG-AGAAGAACACCCAAAACGCGTAGCAGCT
301300 TTGGGGACAAAAATCGAAAACCTAATCCCCAAAATCACCT
64 TTGGGGACAAAAATCGAAAACCTAATCCCCAAAATCACCT
301340 AGCCGGGCCT
Statistics
Matches: 93, Mismatches: 8, Indels: 7
0.86 0.07 0.06
Matches are distributed among these distances:
104 23 0.25
106 1 0.01
107 56 0.60
108 13 0.14
ACGTcount: A:0.40, C:0.26, G:0.20, T:0.14
Consensus pattern (104 bp):
GCTGGAGAGAAAGAAACGGACTCACCAAAAACTAGAGAAGAACACCCAAAACGCGTAGCAGCTTT
GGGGACAAAAATCGAAAACCTAATCCCCAAAATCACCTG
Found at i:309731 original size:31 final size:31
Alignment explanation
Indices: 309696--309768 Score: 87
Period size: 30 Copynumber: 2.4 Consensus size: 31
309686 AAAAATATAA
* *
309696 TTTTGGTCACTTACG-TTATTGTTTTATTAGG
1 TTTTGGTCACTT-CGATTATCGTTTTATTAAG
**
309727 TTTTGACCAC-TCGATTATCGTTTTATTAAG
1 TTTTGGTCACTTCGATTATCGTTTTATTAAG
309757 TTTTGGTCACTT
1 TTTTGGTCACTT
309769 GGACGTTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
29 2 0.06
30 23 0.68
31 9 0.26
ACGTcount: A:0.18, C:0.14, G:0.16, T:0.52
Consensus pattern (31 bp):
TTTTGGTCACTTCGATTATCGTTTTATTAAG
Found at i:310851 original size:31 final size:31
Alignment explanation
Indices: 310813--310880 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
310803 CGGTAATCAC
* **
310813 ATCTTAATTAAAACGAAATGAAAGTGATTAA
1 ATCTTAATCAAAACGAAACAAAAGTGATTAA
*
310844 ATCTTAATCAAAACGAAACAAAATTGATTAA
1 ATCTTAATCAAAACGAAACAAAAGTGATTAA
310875 ATCTTA
1 ATCTTA
310881 TGTTTTTTGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.29
Consensus pattern (31 bp):
ATCTTAATCAAAACGAAACAAAAGTGATTAA
Found at i:311704 original size:3 final size:3
Alignment explanation
Indices: 311685--311736 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
311675 TAGTCCGGGT
* * * *
311685 TTA TATA TTA CTA TTA TTA TTA CTA TTA CTA TTA TTA CTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
311731 TTA TTA
1 TTA TTA
311737 CATTTGCAGC
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:311711 original size:9 final size:9
Alignment explanation
Indices: 311690--311736 Score: 67
Period size: 9 Copynumber: 5.2 Consensus size: 9
311680 CGGGTTTATA
311690 TATTACTAT
1 TATTACTAT
* *
311699 TATTATTAC
1 TATTACTAT
311708 TATTACTAT
1 TATTACTAT
311717 TATTACTAT
1 TATTACTAT
*
311726 TATTATTAT
1 TATTACTAT
311735 TA
1 TA
311737 CATTTGCAGC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (9 bp):
TATTACTAT
Found at i:311719 original size:15 final size:15
Alignment explanation
Indices: 311699--311737 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
311689 ATATTACTAT
311699 TATTATTACTATTAC
1 TATTATTACTATTAC
*
311714 TATTATTACTATTAT
1 TATTATTACTATTAC
311729 TATTATTAC
1 TATTATTAC
311738 ATTTGCAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.33, C:0.10, G:0.00, T:0.56
Consensus pattern (15 bp):
TATTATTACTATTAC
Found at i:320155 original size:52 final size:52
Alignment explanation
Indices: 320089--320187 Score: 144
Period size: 52 Copynumber: 1.9 Consensus size: 52
320079 ATTGAAGGTC
* ** *
320089 TATATTATATATGTGGGACATCTTGAAGGTTCACATCAACATGAAAAAGACA
1 TATATTATACATGTGGGACATCTTGAAGACTCACACCAACATGAAAAAGACA
* *
320141 TATATTATCCATGTGGGGCATCTTGAAGACTCACACCAACATGAAAA
1 TATATTATACATGTGGGACATCTTGAAGACTCACACCAACATGAAAA
320188 GGTTGGGATA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 41 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (52 bp):
TATATTATACATGTGGGACATCTTGAAGACTCACACCAACATGAAAAAGACA
Found at i:321578 original size:40 final size:40
Alignment explanation
Indices: 321534--321931 Score: 629
Period size: 40 Copynumber: 10.0 Consensus size: 40
321524 ATTTCATTTT
321534 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
321574 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
321614 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* *
321654 ACTCAAGATTGTTTTTCCTTGAAACATAAGATTTTATTTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* * *
321694 ATTCAAGATTGCTTTTCCTTGAAACAAAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* * *
321734 ACTCAAGATTTTTTTTCCTTGAAACATAAGATTTTATCTT
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* * *
321774 AGTCAAGATTGTTTTTCCTTGAAATAAAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
321814 ACTCAAGATTGTTTTTCCTTGAAACAGAAGA-TTT-TCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* *
321852 ATTCAAGATTGTTTTTCCTTGAAACATAAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
* * * *
321892 ACTCAAGATTGGTTTTCCTCGAAATAGGAGATTTTATCTC
1 ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
321932 GCTTGAGATA
Statistics
Matches: 329, Mismatches: 27, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
38 33 0.10
39 6 0.02
40 290 0.88
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (40 bp):
ACTCAAGATTGTTTTTCCTTGAAACAGAAGATTTTATCTC
Found at i:322011 original size:37 final size:37
Alignment explanation
Indices: 321922--322038 Score: 155
Period size: 37 Copynumber: 3.2 Consensus size: 37
321912 GAAATAGGAG
* * *
321922 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-AA
1 ATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACAAA
*
321958 ATATTGTCTCCCTTGAGATAGTTTCTCTTGAAACAAA
1 ATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACAAA
* *
321995 ATTTTGTCTCCCTTGAGACAGTTTCTTTTGAAACATAA
1 ATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA-AA
*
322033 ACTTTG
1 ATTTTG
322039 AAAACGTTTC
Statistics
Matches: 71, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
36 30 0.42
37 34 0.48
38 7 0.10
ACGTcount: A:0.27, C:0.19, G:0.14, T:0.40
Consensus pattern (37 bp):
ATTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACAAA
Found at i:322141 original size:65 final size:66
Alignment explanation
Indices: 322072--322195 Score: 198
Period size: 65 Copynumber: 1.9 Consensus size: 66
322062 TTTGTCTCTC
* *
322072 TTGAGACAT-TTTCCCTTGAAACAAATTTTGTCT-CCTTGAGATAGTTTCTCTTGAAACACAAAA
1 TTGAGA-ATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAA
322135 TT
65 TT
*
322137 TTGAGAATGTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACA
1 TTGAGAATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACA
322196 AATTTTTGTC
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
64 2 0.04
65 29 0.54
66 23 0.43
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (66 bp):
TTGAGAATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACAAAAT
T
Found at i:322164 original size:101 final size:101
Alignment explanation
Indices: 321934--322226 Score: 392
Period size: 101 Copynumber: 2.9 Consensus size: 101
321924 TTTATCTCGC
* * *
321934 TTGAG-ATAGTTTCCCTTGAAACAAATATTGTCTCCCTTGAGATAGTTTCTCTTGAAACAAAATT
1 TTGAGAAT-GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAAC-AAATT
* * *
321998 TTGTCTCCCTTGAGACAGTTTCTTTTGAAACATAAACT
64 TTGTCTCCCTTGAGATAGTTTCTCTTGAAACAAAAACT
* * * * *
322036 TTGAAAACGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACATTTTCCCTTGAAACAAATTTT
1 TTGAGAATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAATTTT
*
322101 GTCT-CCTTGAGATAGTTTCTCTTGAAACACAAAATT
66 GTCTCCCTTGAGATAGTTTCTCTTGAAACA-AAAACT
*
322137 TTGAGAATGTTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAATTTT
1 TTGAGAATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAA-TTT
* * *
322202 TGTCTCCCTTAAAATAGTTTTTCTT
65 TGTCTCCCTTGAGATAGTTTCTCTT
322227 AAAATCAACT
Statistics
Matches: 167, Mismatches: 20, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
100 23 0.14
101 70 0.42
102 57 0.34
103 17 0.10
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (101 bp):
TTGAGAATGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAAATTTT
GTCTCCCTTGAGATAGTTTCTCTTGAAACAAAAACT
Found at i:322191 original size:36 final size:35
Alignment explanation
Indices: 321922--322289 Score: 228
Period size: 36 Copynumber: 10.5 Consensus size: 35
321912 GAAATAGGAG
* *
321922 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACAA
1 ATTTTGTCTC-CTTGAGACAGTTTCCCTTGAAACAA
* * *
321958 ATATTGTCTCCCTTGAGATAGTTTCTCTTGAAACAAA
1 ATTTTGTCT-CCTTGAGACAGTTTCCCTTGAAAC-AA
**
321995 ATTTTGTCTCCCTTGAGACAGTTTCTTTTGAAACATA
1 ATTTTGTCT-CCTTGAGACAGTTTCCCTTGAAACA-A
* *
322032 A-----ACT--TTGA-AAACGTTTCCCTTGAAACAA
1 ATTTTGTCTCCTTGAGACA-GTTTCCCTTGAAACAA
*
322060 ATTTTGTCTCTCTTGAGACATTTTCCCTTGAAACAA
1 ATTTTGTCTC-CTTGAGACAGTTTCCCTTGAAACAA
* *
322096 ATTTTGTCTCCTTGAGATAGTTTCTCTTGAAACACA
1 ATTTTGTCTCCTTGAGACAGTTTCCCTTGAAACA-A
** *
322132 A---AAT-T--TTGAGA-ATGTTTCCCTTGAAACGA
1 ATTTTGTCTCCTTGAGACA-GTTTCCCTTGAAACAA
* *
322161 ATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACAA
1 ATTTTGTCT-CCTTGAGACAGTTTCCCTTGAAACAA
* * * ** *
322197 ATTTTTGTCTCCCTTAAAATAGTTTTTCTTAAAATC-A
1 A-TTTTGTCT-CCTTGAGACAGTTTCCCTTGAAA-CAA
* * * *
322234 ACTTCGTCTCGCTTGAGACATTTTTCTCTTGAAACAA
1 ATTTTGTCTC-CTTGAGACA-GTTTCCCTTGAAACAA
322271 AGTTTTGTCTCCCTTGAGA
1 A-TTTTGTCT-CCTTGAGA
322290 TGGTTTTTCT
Statistics
Matches: 261, Mismatches: 41, Indels: 58
0.73 0.11 0.16
Matches are distributed among these distances:
28 4 0.02
29 20 0.08
30 19 0.07
32 4 0.02
33 4 0.02
35 22 0.08
36 94 0.36
37 79 0.30
38 14 0.05
39 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (35 bp):
ATTTTGTCTCCTTGAGACAGTTTCCCTTGAAACAA
Found at i:322296 original size:74 final size:73
Alignment explanation
Indices: 322166--322338 Score: 229
Period size: 74 Copynumber: 2.4 Consensus size: 73
322156 AACGAATTTT
* *
322166 GTCTCCCTTGAGACAATTTCTCTTGAAACAAATTTTTGTCTCCCTTAAAATAGTTTTTCTTAAAA
1 GTCTCGCTTGAGACAATTTCTCTTGAAACAAAGTTTTGTCTCCCTTAAAATAGTTTTTCTTAAAA
*
322231 TCAACTTC
66 CCAACTTC
* * * *
322239 GTCTCGCTTGAGACATTTTTCTCTTGAAACAAAGTTTTGTCTCCCTTGAGATGGTTTTTCTTAAA
1 GTCTCGCTTGAGACA-ATTTCTCTTGAAACAAAGTTTTGTCTCCCTTAAAATAGTTTTTCTTAAA
*
322304 ACCTACTTC
65 ACCAACTTC
* * * *
322313 TTCTTGCTTGAGACAATCTCCCTTGA
1 GTCTCGCTTGAGACAATTTCTCTTGA
322339 GACAGTCTCG
Statistics
Matches: 86, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
73 22 0.26
74 64 0.74
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (73 bp):
GTCTCGCTTGAGACAATTTCTCTTGAAACAAAGTTTTGTCTCCCTTAAAATAGTTTTTCTTAAAA
CCAACTTC
Found at i:322339 original size:15 final size:15
Alignment explanation
Indices: 322319--322359 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
322309 CTTCTTCTTG
322319 CTTGAGACAATCTCC
1 CTTGAGACAATCTCC
* *
322334 CTTGAGACAGTCTCG
1 CTTGAGACAATCTCC
322349 CTTGAGACAAT
1 CTTGAGACAAT
322360 TTTCATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.27
Consensus pattern (15 bp):
CTTGAGACAATCTCC
Found at i:322464 original size:60 final size:61
Alignment explanation
Indices: 322349--322468 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 61
322339 GACAGTCTCG
* * *
322349 CTTGAGACAATTTTCATTTAAAACAAAATTTATCTCACTTGAGATGGTTTTTCTTAAAACC
1 CTTGAGACAATTTTCACTTAAAACAAAATTTATCTCACTTGAGATGGCTTCTCTTAAAACC
* *
322410 CTTGAGACAATTTTC-CTTCAAATAAAATTTATCTCA-TTCGAGA-GAGCTTCTCTTAAAAC
1 CTTGAGACAATTTTCACTTAAAACAAAATTTATCTCACTT-GAGATG-GCTTCTCTTAAAAC
322469 AAGTTTCTTA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
59 3 0.06
60 34 0.65
61 15 0.29
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (61 bp):
CTTGAGACAATTTTCACTTAAAACAAAATTTATCTCACTTGAGATGGCTTCTCTTAAAACC
Found at i:322990 original size:118 final size:118
Alignment explanation
Indices: 322843--323169 Score: 469
Period size: 117 Copynumber: 2.8 Consensus size: 118
322833 CTCGCTTGAG
*
322843 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTC
1 GGATCAACATTTACAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTC
* **
322908 ATAATGAGAAGAACTTGTTCAACCTTGGTTTCAAGCCCACCGTAGAAGGAGAT
66 ATAATGAGAAGAACTTGTTCAACCTTGGATTCAAGCCCACCACAGAAGGAGAT
* * * * * * *
322961 -GACTCAACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCGTCCAATGAGGGAGGATAATTT
1 GGA-TCAACATTTACAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTT
* * ** * *
323025 CATAATGAGAAGAACTTGTTAAACCTT-GATTCGATTCCATCACAGAAGGAGGT
65 CATAATGAGAAGAACTTGTTCAACCTTGGATTCAAGCCCACCACAGAAGGAGAT
*
323078 GGATCAACATTTACAGTGGAGAGTTCATAATGAGAAGAACTCATCCAAAGAGGAAGAAGAAGTTC
1 GGATCAACATTTACAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTC
323143 ATAATGAGAAGAACTTGTTCAACCTTG
66 ATAATGAGAAGAACTTGTTCAACCTTG
323170 CATCAGTATT
Statistics
Matches: 181, Mismatches: 25, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
117 99 0.55
118 82 0.45
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (118 bp):
GGATCAACATTTACAGTGGAGAGTTCATAATGAGAAGAACTCATCCAATGAGGAAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTGGATTCAAGCCCACCACAGAAGGAGAT
Found at i:323162 original size:20 final size:20
Alignment explanation
Indices: 323099--323163 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
323089 TACAGTGGAG
323099 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
* **
323119 CA-TCCA-AA-GAGGAAGAAGA
1 -AGTTCATAATGA-GAAGAACT
323138 AGTTCATAATGAGAAGAACT
1 AGTTCATAATGAGAAGAACT
*
323158 TGTTCA
1 AGTTCA
323164 ACCTTGCATC
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.45, C:0.12, G:0.22, T:0.22
Consensus pattern (20 bp):
AGTTCATAATGAGAAGAACT
Found at i:323253 original size:20 final size:19
Alignment explanation
Indices: 323191--323254 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 19
323181 CCAATGAAGA
323191 GTTCATAATGAGAAGAACT
1 GTTCATAATGAGAAGAACT
* * *
323210 CATCCAATAAGAGAGAAGAA--
1 -GTTC-ATAA-TGAGAAGAACT
323230 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAAC-T
323250 GTTCA
1 GTTCA
323255 ATCCAATGCT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
17 8 0.24
18 4 0.12
19 2 0.06
20 7 0.21
21 4 0.12
22 8 0.24
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.23
Consensus pattern (19 bp):
GTTCATAATGAGAAGAACT
Found at i:323417 original size:3 final size:3
Alignment explanation
Indices: 323404--323482 Score: 104
Period size: 3 Copynumber: 26.0 Consensus size: 3
323394 TAGTCCGAGT
* *
323404 TTA TATA TTA TTA TTA TTA TTA TTA CTA TTA TTA TTA CTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
323450 TTA CTA TTA CTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
323483 CATTTGTAGG
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 62 0.95
4 3 0.05
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:327622 original size:19 final size:19
Alignment explanation
Indices: 327588--327624 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
327578 ATATCTCATT
327588 TTTATCTTTCACTTTTATA
1 TTTATCTTTCACTTTTATA
327607 TTTA-CTTTCACATTTTAT
1 TTTATCTTTCAC-TTTTAT
327625 TTTCATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATCTTTCACTTTTATA
Found at i:327727 original size:19 final size:19
Alignment explanation
Indices: 327687--327736 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
327677 GTTTCTGGAC
*
327687 TCATAACTTAATTTCATAT
1 TCATAGCTTAATTTCATAT
*
327706 TCATAGCTTATTTTCA-AGT
1 TCATAGCTTAATTTCATA-T
*
327725 TCATAGCCTAAT
1 TCATAGCTTAAT
327737 GCATATTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 1 0.04
19 25 0.96
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (19 bp):
TCATAGCTTAATTTCATAT
Found at i:330673 original size:31 final size:30
Alignment explanation
Indices: 330629--330686 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
330619 AAAAACACCT
330629 AACTTTTGAAAATTA-CACTTTTGGTCCATA
1 AACTTTTGAAAATTAGC-CTTTTGGTCCATA
330659 AACTTTTAGAAAATTAGCCTTTTGGTCC
1 AACTTTT-GAAAATTAGCCTTTTGGTCC
330687 CTATTTAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 7 0.27
31 18 0.69
32 1 0.04
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (30 bp):
AACTTTTGAAAATTAGCCTTTTGGTCCATA
Found at i:332048 original size:25 final size:25
Alignment explanation
Indices: 332020--332073 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
332010 ATTAATTGAG
332020 ACTTACAAAATTTAAATTAGTCAAA
1 ACTTACAAAATTTAAATTAGTCAAA
* * *
332045 ACTTACAAATTTTAGATTAGTCGAA
1 ACTTACAAAATTTAAATTAGTCAAA
332070 ACTT
1 ACTT
332074 TATGTGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.35
Consensus pattern (25 bp):
ACTTACAAAATTTAAATTAGTCAAA
Found at i:332461 original size:24 final size:26
Alignment explanation
Indices: 332429--332481 Score: 76
Period size: 24 Copynumber: 2.1 Consensus size: 26
332419 ATGTATATTA
332429 ATTTTTTTAAT-TTT--ATATTTTTAT
1 ATTTTTTTAATATTTGAATA-TTTTAT
332453 ATTTTTTTAATATTTGAATATTTTAT
1 ATTTTTTTAATATTTGAATATTTTAT
332479 ATT
1 ATT
332482 AAAATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 11 0.42
25 3 0.12
26 9 0.35
27 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
ATTTTTTTAATATTTGAATATTTTAT
Found at i:332467 original size:26 final size:24
Alignment explanation
Indices: 332429--332481 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 24
332419 ATGTATATTA
*
332429 ATTTTTTTAATTT-TATATTTTTAT
1 ATTTTTTTAATTTGAATA-TTTTAT
332453 ATTTTTTTAATATTTGAATATTTTAT
1 ATTTTTTT-A-ATTTGAATATTTTAT
332479 ATT
1 ATT
332482 AAAATTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 8 0.32
25 1 0.04
26 13 0.52
27 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
ATTTTTTTAATTTGAATATTTTAT
Found at i:338067 original size:23 final size:23
Alignment explanation
Indices: 338041--338084 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
338031 ATTCCCCTAG
338041 GGGGAATCGGTTCCCATTCAAAT
1 GGGGAATCGGTTCCCATTCAAAT
*
338064 GGGGAATCGGTTCCCCTTCAA
1 GGGGAATCGGTTCCCATTCAA
338085 GGGGGTATCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (23 bp):
GGGGAATCGGTTCCCATTCAAAT
Found at i:344546 original size:20 final size:20
Alignment explanation
Indices: 344499--344664 Score: 135
Period size: 20 Copynumber: 8.2 Consensus size: 20
344489 AATGACCAAC
344499 AAAATCGCAACGCGATATC--
1 AAAATCGCAACGCGAT-TCAG
* *
344518 AAAACCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* * **
344538 AAAAGCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
*
344558 AAGATCGCAACGCGATCTTCCA-
1 AAAATCGCAACGCGA--TT-CAG
* * *
344580 AGAATCGCAATGCGATTCAT
1 AAAATCGCAACGCGATTCAG
*
344600 AAAATCGCAACGCGATTAAG
1 AAAATCGCAACGCGATTCAG
344620 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
344640 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
344660 AAAAT
1 AAAAT
344665 GAGTAAATTC
Statistics
Matches: 116, Mismatches: 21, Indels: 19
0.74 0.13 0.12
Matches are distributed among these distances:
18 1 0.01
19 21 0.18
20 78 0.67
21 3 0.03
22 12 0.10
23 1 0.01
ACGTcount: A:0.41, C:0.23, G:0.19, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:344647 original size:82 final size:81
Alignment explanation
Indices: 344501--344655 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 81
344491 TGACCAACAA
* * *
344501 AATCGCAACGCGATATCAAAACCGCAACGCGATTTAGAAAAGCGCAACGTTGAAAAGAAGATCGC
1 AATCGCAACGCGATATCAAAACCGCAACGCGATTAAGAAAAGCGCAACGTCGAAAACAAGATCGC
344566 AACGCGATCTTCCAAG
66 AACGCGATCTTCCAAG
* * * ***
344582 AATCGCAATGCGAT-TCATAAAATCGCAACGCGATTAAGAAAATCGCAACG-CGATTCCAAGAAT
1 AATCGCAACGCGATATC--AAAACCGCAACGCGATTAAGAAAAGCGCAACGTCGAAAACAAG-AT
344645 CGCAACGCGAT
63 CGCAACGCGAT
344656 TCAGAAAATG
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
80 2 0.03
81 18 0.29
82 42 0.68
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (81 bp):
AATCGCAACGCGATATCAAAACCGCAACGCGATTAAGAAAAGCGCAACGTCGAAAACAAGATCGC
AACGCGATCTTCCAAG
Found at i:344771 original size:6 final size:6
Alignment explanation
Indices: 344760--344791 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
344750 GACACGTATT
344760 ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
344792 CGAGACGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.31, C:0.53, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:345408 original size:6 final size:6
Alignment explanation
Indices: 345285--345407 Score: 201
Period size: 6 Copynumber: 20.5 Consensus size: 6
345275 TCTCGTCTCG
345285 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
*
345333 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTAGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
* * * *
345381 GGTAGT GGTAGT GGTAGT GGTAGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGT
345408 AATACGTGTC
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 116 1.00
ACGTcount: A:0.04, C:0.12, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:347566 original size:38 final size:38
Alignment explanation
Indices: 347508--347596 Score: 135
Period size: 38 Copynumber: 2.3 Consensus size: 38
347498 TTTATTTTGT
*
347508 TCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGAG
1 TCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
*
347545 TCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGGG
1 TCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
*
347583 TCGGGTTCGGGTTT
1 TC-GGATCGGGTTT
347597 AGGGTGAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
37 9 0.19
38 28 0.60
39 10 0.21
ACGTcount: A:0.11, C:0.11, G:0.38, T:0.39
Consensus pattern (38 bp):
TCGGATCGGGTTTTTTTAAGTGTGATATTCGGGTCGAG
Found at i:348036 original size:167 final size:169
Alignment explanation
Indices: 347572--348099 Score: 920
Period size: 168 Copynumber: 3.1 Consensus size: 169
347562 AAGTGTGATA
*
347572 TTCGGGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACTGGACCCGACCCGAAAAAAATATATAA
1 TTCGTGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACTGGACCCGACCCGAAAAAAATATATAA
*
347637 TTTTACCTTATATATTTAGAAATAATTACAATAATACCCCTCTATATATAAGTTTTTTCAATTAA
66 TTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAAGTTTTTTCAATTAA
347702 GTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTAT
131 GTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTAT
* *
347741 TTCGTGTCGGGTCGGGTTTGGGTTTAGGGTGAAAAAATTGGACCCGACCCG-AAAAAATATATAA
1 TTCGTGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACTGGACCCGACCCGAAAAAAATATATAA
* *
347805 TTTTACCTTATATATTTATGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAA
66 TTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAAGTTTTTTCAATTAA
*
347870 GTCAATGTTTTTATTGAATAAAAATAACTTTTTTATTAT
131 GTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTAT
* * **
347909 TTCATGTCGGGTCGAG-TCGGGTTTAGGGTGAAAAAACTCTACCCGACCCGAAAAAAATATATAA
1 TTCGTGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACTGGACCCGACCCGAAAAAAATATATAA
347973 TTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAA-TTTTTTCAATTAA
66 TTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAAGTTTTTTCAATTAA
348037 GTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTAT
131 GTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTAT
*
348076 TTCGTGTCGTGTCGGG-TCGGGTTT
1 TTCGTGTCGGGTCGGGTTCGGGTTT
348100 CTAATTCATA
Statistics
Matches: 340, Mismatches: 18, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
167 102 0.30
168 190 0.56
169 48 0.14
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (169 bp):
TTCGTGTCGGGTCGGGTTCGGGTTTAGGGTGAAAAAACTGGACCCGACCCGAAAAAAATATATAA
TTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATAAGTTTTTTCAATTAA
GTCAATGTTTTTATTGAATAAAAATAATTTTTTTATTAT
Found at i:357765 original size:20 final size:19
Alignment explanation
Indices: 357742--357788 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
357732 CGATATACCA
*
357742 GGTAAAAATATGATAAAATC
1 GGTAAAAA-ATGATAAAACC
*
357762 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
357782 GGTAAAA
1 GGTAAAA
357789 CGTTATCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:357865 original size:181 final size:182
Alignment explanation
Indices: 357530--358002 Score: 723
Period size: 181 Copynumber: 2.6 Consensus size: 182
357520 GATCCAAATT
* * * **
357530 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAATCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
* * * * * * *
357595 AAATCGGTAAAGCGCTACCAGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* *
357660 GTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
*
357712 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
* * *
357777 AAACCGGTAAAACGTTATCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
357841 GTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
131 GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* * *
357893 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
357958 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
358003 CGTAAGTACG
Statistics
Matches: 265, Mismatches: 26, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
181 169 0.64
182 96 0.36
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAATCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:357946 original size:20 final size:19
Alignment explanation
Indices: 357923--357969 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
357913 CGATATAACA
357923 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
357943 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
357963 GGTAAAA
1 GGTAAAA
357970 CGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:357974 original size:17 final size:19
Alignment explanation
Indices: 357934--357974 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
357924 GTAAAAATAT
*
357934 GATAAAACCGGTATCAAAAT
1 GATAAAACCGG-ATCAAAAC
357954 GATAAAACCGG-T-AAAAC
1 GATAAAACCGGATCAAAAC
357971 GATA
1 GATA
357975 CCGGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
20 11 0.55
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
GATAAAACCGGATCAAAAC
Found at i:360225 original size:21 final size:21
Alignment explanation
Indices: 360199--360281 Score: 139
Period size: 21 Copynumber: 4.0 Consensus size: 21
360189 AAGACAATCA
360199 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
360220 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
*
360241 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAT
* *
360262 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGAGAAACTTGA
360282 GAGGCATAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:360357 original size:33 final size:33
Alignment explanation
Indices: 360315--360383 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
360305 GAAAAATAGA
*
360315 TGAAGTGGTGAAAGAAGTAGAGGTGTTGAGGGG
1 TGAAGTGGTGAAAGAAGTAGAGGTGTTAAGGGG
* *
360348 TGAAGTGGTGAAAGAAGTTGGGGTGTTAAGGGG
1 TGAAGTGGTGAAAGAAGTAGAGGTGTTAAGGGG
360381 TGA
1 TGA
360384 TATTAAGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.29, C:0.00, G:0.48, T:0.23
Consensus pattern (33 bp):
TGAAGTGGTGAAAGAAGTAGAGGTGTTAAGGGG
Found at i:361002 original size:183 final size:183
Alignment explanation
Indices: 360656--361244 Score: 1038
Period size: 183 Copynumber: 3.2 Consensus size: 183
360646 CAAAGTTTTC
*
360656 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
360721 CAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
*
360784 TATAATCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
360840 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCATAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
360905 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
360970 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
361023 ACCCTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
361088 CAAAAAGTGTCGACATTTACACACCGGAACCCAGAATTATAATGTAATAGATAATTTTATATTAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
361153 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
361206 ACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAGAAT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAAT
361245 TATAATGTAC
Statistics
Matches: 390, Mismatches: 13, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
183 312 0.80
184 75 0.19
186 3 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:361331 original size:120 final size:120
Alignment explanation
Indices: 361118--361364 Score: 431
Period size: 120 Copynumber: 2.1 Consensus size: 120
361108 ACACCGGAAC
*
361118 CCAGAATTATAATGTAATAGATAATTTTATATTATAACCGGTATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGC
*
361183 GAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* * * *
361238 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGC
*
361303 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
361358 CCAGAAT
1 CCAGAAT
361365 GGAAGAAAAA
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:361482 original size:303 final size:303
Alignment explanation
Indices: 360935--361831 Score: 1668
Period size: 303 Copynumber: 3.0 Consensus size: 303
360925 ACATCGGAAC
* * *
360935 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
* *
361000 GAATAGGTCTACAACCTATATCGACCCTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
*
361065 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACACCGGAACCCAGAATTATAA
131 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
* *
361130 TGTAATAGATAATTTTATATTATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
196 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
361195 AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
261 AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
361238 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
1 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
361303 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
*
361368 AGAAAAATGTGTCGATACCTTGTCTAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
131 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
*
361433 TGTAATAGATAATTTTGTAATATAACCGATATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
196 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
361498 AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
261 AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
*
361541 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCAGTTTTATTAGC
1 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
361606 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
66 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
* *
361671 AGAAAAATGTGTCGATACTTTGTCAAAAAGTATCGACATTTACACATCGGAACCCAGAATTATAA
131 AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
361736 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
196 TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
*
361801 AACCTATATCGACACTTTTTAATATTGTGTC
261 AACCTATATCGACACTTTTTAATTTTGTGTC
361832 ACTAATTTTA
Statistics
Matches: 578, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
303 578 1.00
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (303 bp):
CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGC
GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGA
AGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAA
TGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTAC
AACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
Found at i:361634 original size:120 final size:120
Alignment explanation
Indices: 361421--361667 Score: 431
Period size: 120 Copynumber: 2.1 Consensus size: 120
361411 ACATCGGAAC
*
361421 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCGGTTTTATGAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCAGTTTTATGAGC
*
361486 GAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
* * * *
361541 CCAGAATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCAGTTTTATTAGC
1 CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCAGTTTTATGAGC
*
361606 GAATAGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGT
66 GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
361661 CCAGAAT
1 CCAGAAT
361668 GGAAGAAAAA
Statistics
Matches: 120, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (120 bp):
CCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATATACCAGTTTTATGAGC
GAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGT
Found at i:361730 original size:486 final size:484
Alignment explanation
Indices: 360656--361831 Score: 1404
Period size: 486 Copynumber: 2.4 Consensus size: 484
360646 CAAAGTTTTC
360656 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATA-CTTTT
* *** *
360721 CAAAAAGTGTCGATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATA
65 CAAAAAGTGTCGA--CATTTAACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATA
*
360786 TAATCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAA
128 TAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAA
*
360851 TATTGTGTCGGTACTTTATGTCCATAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTC
193 TATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTC
*
360916 GACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAA
258 GACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGATATAA
*
360981 ATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACCCTTTTTAATATTGTGTCGGT
323 ATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
* * * * **
361046 ACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACA
388 ACTTTATGTCCAGAAT----GAAAAATGTCTAGATACCTTGT---AAAGTATCAACAGGTACACA
* *** *
361111 CCGGAACCCAGAATTATAATGTAATAGATAATTTTATATT
446 -CGGAACCCAGAATTATAATGGAATAGATAAACCTATATG
* ** * * ** ** *** ** * * *
361151 ATAACCGGTATAA-A-TATACCGGT--TTTATGAGC-GAATAGGTCTACAACCTATATCGACACT
1 A-CA-CTTTTTAATATTGTGTCGGTACTTTATGTCCAGAAT-GGAAGA-AAAATGTGTCGATACT
* *** * *
361211 TTTTAATTTTGTGTCGGTAC-TTT---AT--G--TCCAGAATTATAATGTACTAGATAATTTTGT
62 TTTCAA-AAAGTGTC-G-ACATTTAACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGT
* * *
361268 AATATAACCGGTATAAGTATACCGGTTTTATTAGCGAATAGGTCTACAACCTATGTCGACACTTT
124 AATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTT
*
361333 TTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCTAAAAG
189 TTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAG
361398 TGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGAT
254 TGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGAT
*
361463 ATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATTTTGTGT
319 ATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGT
* * ** * *
361528 CGGTACTTTATGTCCAGAAT-TATAATGTACTAGATAATTTTGT-AA-TAT-AACCGGTATA-A-
384 CGGTACTTTATGTCCAGAATGAAAAATGT-CTAGAT-ACCTTGTAAAGTATCAACAGGTACACAC
* ** * * *
361587 GTATA-CCAGTTTTATTA-GCGAATAGGTCTACAACCTATGTCG
447 GGA-ACCCAGAATTATAATG-GAATA-G-ATA-AACCTATAT-G
361629 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACTTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACTTT-T
*
361694 CAAAAAGTATCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
65 CAAAAAGTGTCGACATTTA-ACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
361759 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
129 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
361824 ATTGTGTC
194 ATTGTGTC
361832 ACTAATTTTA
Statistics
Matches: 564, Mismatches: 87, Indels: 69
0.78 0.12 0.10
Matches are distributed among these distances:
473 1 0.00
474 15 0.03
475 2 0.00
476 8 0.01
477 14 0.02
478 13 0.02
479 19 0.03
480 13 0.02
481 10 0.02
482 6 0.01
483 5 0.01
484 1 0.00
486 403 0.71
488 1 0.00
490 2 0.00
492 4 0.01
493 17 0.03
494 14 0.02
495 8 0.01
496 3 0.01
497 5 0.01
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (484 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACTTTTC
AAAAAGTGTCGACATTTAACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAA
CCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATAT
TGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGTCAAAAAGTGTCGAC
ATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAACCGATATAAATA
TACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACT
TTATGTCCAGAATGAAAAATGTCTAGATACCTTGTAAAGTATCAACAGGTACACACGGAACCCAG
AATTATAATGGAATAGATAAACCTATATG
Found at i:365285 original size:87 final size:87
Alignment explanation
Indices: 365181--365434 Score: 458
Period size: 87 Copynumber: 2.9 Consensus size: 87
365171 AAATAGGTCA
* *
365181 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
365246 CCCGTTAAATACATATTTTATT
66 CCCGTTAAATACATATTTTATT
365268 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
365333 CCCGTTAAATATC-TATTTTATT
66 CCCGTTAAATA-CATATTTTATT
365355 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
*
365420 CCGGTTAAATA-ATAT
66 CCCGTTAAATACATAT
365435 AACATAACTG
Statistics
Matches: 162, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
86 3 0.02
87 158 0.98
88 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTATCTATTACATTATATAAGCGTTACCTAATATGTTATTGTACTTGATAATATTT
CCCGTTAAATACATATTTTATT
Found at i:365315 original size:23 final size:23
Alignment explanation
Indices: 365265--365309 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
365255 TACATATTTT
* *
365265 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
365288 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
365310 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:365368 original size:23 final size:23
Alignment explanation
Indices: 365342--365386 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
365332 TCCCGTTAAA
**
365342 TATCTATTTTATTATATAAGCGC
1 TATCTATTACATTATATAAGCGC
365365 TATCTATTACATTATATAAGCG
1 TATCTATTACATTATATAAGCG
365387 TTACCTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.44
Consensus pattern (23 bp):
TATCTATTACATTATATAAGCGC
Found at i:365402 original size:23 final size:23
Alignment explanation
Indices: 365352--365396 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
365342 TATCTATTTT
* *
365352 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
365375 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
365397 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:365644 original size:29 final size:29
Alignment explanation
Indices: 365603--365670 Score: 68
Period size: 31 Copynumber: 2.3 Consensus size: 29
365593 GTATCATTTT
*
365603 TATCATTGAATTT-TTAAA-AATTATAAAA
1 TATCATT-AATTTATCAAATAATTATAAAA
*
365631 TGATCATTATATTTATCAAATTATTATAAAA
1 T-ATCATTA-ATTTATCAAATAATTATAAAA
365662 TAGTCATTA
1 TA-TCATTA
365671 CAATATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
28 2 0.06
29 10 0.30
30 5 0.15
31 16 0.48
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (29 bp):
TATCATTAATTTATCAAATAATTATAAAA
Found at i:365740 original size:31 final size:29
Alignment explanation
Indices: 365705--365771 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 29
365695 TTTGATAAAT
365705 TTAATGATCATTTTATAATTATTCAAAAAAA
1 TTAATGATCATTTTATAATT-TT-AAAAAAA
* * * *
365736 TTAATAATTATTTTATAATTTTTAAAAAT
1 TTAATGATCATTTTATAATTTTAAAAAAA
365765 TTAATGA
1 TTAATGA
365772 ATAAAACGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 11 0.35
30 2 0.06
31 18 0.58
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
TTAATGATCATTTTATAATTTTAAAAAAA
Found at i:370961 original size:17 final size:16
Alignment explanation
Indices: 370925--370967 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
370915 GATTTTTATT
*
370925 ATTTTTGT-TTAATTA
1 ATTTTTGTATTAATAA
370940 ATTTTTGTATTCAATAA
1 ATTTTTGTATT-AATAA
370957 ATTTTT-TATTA
1 ATTTTTGTATTA
370968 TTTTATTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 9 0.36
16 6 0.24
17 10 0.40
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (16 bp):
ATTTTTGTATTAATAA
Found at i:370961 original size:41 final size:42
Alignment explanation
Indices: 370892--370971 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
370882 TTTTTTTTTA
*
370892 TTAATTTATATTTTATTCAATAAGA-TTTTTATTATTTTTGT
1 TTAATTAATATTTTATTCAATAAGATTTTTTATTATTTTTGT
*
370933 TTAATTAATTTTTGTATTCAATAA-ATTTTTTATTATTTT
1 TTAATTAATATTT-TATTCAATAAGATTTTTTATTATTTT
370972 ATTATTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
41 12 0.34
42 23 0.66
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.64
Consensus pattern (42 bp):
TTAATTAATATTTTATTCAATAAGATTTTTTATTATTTTTGT
Found at i:372812 original size:21 final size:22
Alignment explanation
Indices: 372735--372820 Score: 95
Period size: 22 Copynumber: 4.0 Consensus size: 22
372725 ATGCACAAAG
* *
372735 TCAGATAAAAAATTGATTCGGA
1 TCAGATAAAAAATCGATCCGGA
* * *
372757 T-TGAATAAAAAATTGATCTGGA
1 TCAG-ATAAAAAATCGATCCGGA
*
372779 TCGGATAAAAAATCGATCCGGA
1 TCAGATAAAAAATCGATCCGGA
372801 TCAGAT-AAAAATCGATCCGG
1 TCAGATAAAAAATCGATCCGG
372821 TTTTTTCACA
Statistics
Matches: 55, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
21 15 0.27
22 39 0.71
23 1 0.02
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (22 bp):
TCAGATAAAAAATCGATCCGGA
Found at i:373394 original size:33 final size:33
Alignment explanation
Indices: 373352--373418 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
373342 AGTTTACGGT
* *
373352 AATTGAAATACTTAAATACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
*
373385 AATTCAAATACTTAAAAACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
373418 A
1 A
373419 TTGAAAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:373440 original size:21 final size:21
Alignment explanation
Indices: 373414--373454 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
373404 TTCCAAGTTT
373414 GATAATTGAAAAAAAGTTTAC
1 GATAATTGAAAAAAAGTTTAC
*
373435 GATAATTGAAACAAAGTTTA
1 GATAATTGAAAAAAAGTTTA
373455 AAAATAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.05, G:0.15, T:0.29
Consensus pattern (21 bp):
GATAATTGAAAAAAAGTTTAC
Found at i:376929 original size:23 final size:23
Alignment explanation
Indices: 376880--376930 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
376870 AGGAATGTGC
*
376880 CACAAGAGCATAAAAAAGCGTGG
1 CACAAGAGCATAAAAAAACGTGG
* *
376903 CACAAGAGCATAAAAAAACTTGT
1 CACAAGAGCATAAAAAAACGTGG
376926 CACAA
1 CACAA
376931 TGATATATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.51, C:0.20, G:0.18, T:0.12
Consensus pattern (23 bp):
CACAAGAGCATAAAAAAACGTGG
Done.