Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007749.1 Hibiscus syriacus cultivar Beakdansim tig00110015_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: 1787532
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 8
Found at i:1181718 original size:19 final size:19
Alignment explanation
Indices: 1181659--1181724 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
1181649 TTTACTATCA
*
1181659 CAACGAATTT-GAAAAATTG
1 CAACGAATTTAG-AAAATCG
**
1181678 CAACGCCAATTGTAGACTATCG
1 CAACG--AATT-TAGAAAATCG
1181700 CAACGAATTTAGAAAATCG
1 CAACGAATTTAGAAAATCG
1181719 CAACGA
1 CAACGA
1181725 CAACTGTAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
19 19 0.50
20 4 0.11
21 4 0.11
22 10 0.26
23 1 0.03
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (19 bp):
CAACGAATTTAGAAAATCG
Found at i:1181871 original size:123 final size:123
Alignment explanation
Indices: 1181740--1181978 Score: 345
Period size: 123 Copynumber: 1.9 Consensus size: 123
1181730 GTAGACTATC
* ** * *
1181740 GCAACGCGAAATGGAA-AATCGCAACGCGATTTTCAACTATCGCAACGCGATTTTCAACTATCGC
1 GCAACGCGAAATGCAACAATCGCAACGCGAAATGCAA-AATCGCAACGCGATTTTCAACTATCGC
1181804 AACGCAAAATGGAAAATCGCAACACGATTTTCAACTATCGCAACGCGAAATGGAAAAGT
65 AACGCAAAATGGAAAATCGCAACACGATTTTCAACTATCGCAACGCGAAATGGAAAAGT
** * * *
1181863 GCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCA
1 GCAACGCGAAATGCAACAATCGCAACGCGAAATGCAAAATCGCAACGCGATTTTCAACTATCGCA
* * *
1181928 ATGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
66 ACGCAAAATGGAAAATCGCAACACGATTTTCAACTATCGCAACGCGAAATG
1181979 CAACGCGAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
123 87 0.85
124 15 0.15
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (123 bp):
GCAACGCGAAATGCAACAATCGCAACGCGAAATGCAAAATCGCAACGCGATTTTCAACTATCGCA
ACGCAAAATGGAAAATCGCAACACGATTTTCAACTATCGCAACGCGAAATGGAAAAGT
Found at i:1181995 original size:41 final size:41
Alignment explanation
Indices: 1181778--1181978 Score: 359
Period size: 41 Copynumber: 4.9 Consensus size: 41
1181768 ATTTTCAACT
*
1181778 ATCGCAACGCGATTTTCAACTATCGCAACGCAAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
*
1181819 ATCGCAACACGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1181860 AGT-GCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 A-TCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
*
1181901 ATCGCAACGCGATTTTCAACTATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1181942 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1 ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATG
1181979 CAACGCGAAT
Statistics
Matches: 153, Mismatches: 5, Indels: 4
0.94 0.03 0.02
Matches are distributed among these distances:
40 1 0.01
41 151 0.99
42 1 0.01
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (41 bp):
ATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:1187939 original size:29 final size:29
Alignment explanation
Indices: 1187906--1187990 Score: 134
Period size: 29 Copynumber: 2.9 Consensus size: 29
1187896 TCCCAACACA
1187906 TAGGTCGCCATGCCCTCCGGGCGACTTTG
1 TAGGTCGCCATGCCCTCCGGGCGACTTTG
*
1187935 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCCCTCCGGGCGACTTTG
* * *
1187964 TAGGTCGTCATGCACTCCGGGCTACTT
1 TAGGTCGCCATGCCCTCCGGGCGACTT
1187991 ACCCTCACAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.12, C:0.34, G:0.29, T:0.25
Consensus pattern (29 bp):
TAGGTCGCCATGCCCTCCGGGCGACTTTG
Found at i:1188054 original size:33 final size:33
Alignment explanation
Indices: 1188006--1188078 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
1187996 CACACGGCTT
** * *
1188006 CCCTCGGATTTCCTCGCATAGCTCGCTCGGTTG
1 CCCTCGGATGCCCTCGCATAACTCGCTCGGATG
*
1188039 CCCTCGGATGCCCTCGCATAACTCGTTCGGATG
1 CCCTCGGATGCCCTCGCATAACTCGCTCGGATG
*
1188072 GCCTCGG
1 CCCTCGG
1188079 TCGGATGACC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.37, G:0.26, T:0.26
Consensus pattern (33 bp):
CCCTCGGATGCCCTCGCATAACTCGCTCGGATG
Found at i:1195584 original size:16 final size:16
Alignment explanation
Indices: 1195563--1195609 Score: 94
Period size: 16 Copynumber: 2.9 Consensus size: 16
1195553 TATTGAAATT
1195563 ATACCTCGGCCCAACG
1 ATACCTCGGCCCAACG
1195579 ATACCTCGGCCCAACG
1 ATACCTCGGCCCAACG
1195595 ATACCTCGGCCCAAC
1 ATACCTCGGCCCAAC
1195610 TTGGGCATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.26, C:0.45, G:0.17, T:0.13
Consensus pattern (16 bp):
ATACCTCGGCCCAACG
Found at i:1199206 original size:21 final size:21
Alignment explanation
Indices: 1199180--1199234 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
1199170 CTTGAAATCG
1199180 AAGTAACTAGCAATTCGAGTA
1 AAGTAACTAGCAATTCGAGTA
1199201 AAGTAACTAGCAATTCGAGTA
1 AAGTAACTAGCAATTCGAGTA
*
1199222 AAGTAACTCGCAA
1 AAGTAACTAGCAA
1199235 GTTAACCGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.44, C:0.16, G:0.18, T:0.22
Consensus pattern (21 bp):
AAGTAACTAGCAATTCGAGTA
Found at i:1203177 original size:12 final size:12
Alignment explanation
Indices: 1203160--1203184 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1203150 GTTTGGCAAC
1203160 TTGCCTACACTT
1 TTGCCTACACTT
1203172 TTGCCTACACTT
1 TTGCCTACACTT
1203184 T
1 T
1203185 ATTATGTTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.32, G:0.08, T:0.44
Consensus pattern (12 bp):
TTGCCTACACTT
Found at i:1204084 original size:2 final size:2
Alignment explanation
Indices: 1204077--1204104 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1204067 CTCTGAGAAC
1204077 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
1204105 TGTAACCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1205113 original size:3 final size:3
Alignment explanation
Indices: 1205105--1205134 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1205095 CTACAGATCC
1205105 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1205135 CCTACATATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1206262 original size:27 final size:29
Alignment explanation
Indices: 1206232--1206288 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 29
1206222 GTTCAGAAAG
1206232 TTAT-ACTAAAATTTTAAA-GATATAAAA
1 TTATGACTAAAATTTTAAACGATATAAAA
* *
1206259 TTATGAGTGAAATTTTAAACGATATAAAA
1 TTATGACTAAAATTTTAAACGATATAAAA
1206288 T
1 T
1206289 CAAATAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 4 0.15
28 12 0.46
29 10 0.38
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.37
Consensus pattern (29 bp):
TTATGACTAAAATTTTAAACGATATAAAA
Found at i:1208015 original size:29 final size:29
Alignment explanation
Indices: 1207955--1208021 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
1207945 ATTTCAAATC
*
1207955 TTTTATAATATTTATTATTTTGGGCTTAT
1 TTTTATAATATTTATTATTTAGGGCTTAT
* * *
1207984 TTTTTTAATATTTATTATTATAGGTC-TGT
1 TTTTATAATATTTATTATT-TAGGGCTTAT
1208013 TTTTATAAT
1 TTTTATAAT
1208022 TTATTTTTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 28 0.88
30 4 0.12
ACGTcount: A:0.25, C:0.03, G:0.09, T:0.63
Consensus pattern (29 bp):
TTTTATAATATTTATTATTTAGGGCTTAT
Found at i:1209750 original size:3 final size:3
Alignment explanation
Indices: 1209737--1209801 Score: 114
Period size: 3 Copynumber: 21.7 Consensus size: 3
1209727 ATTTTTCTCT
1209737 TTA TATA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1209782 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
1209802 GTGTTTTGAT
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.03
3 55 0.92
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1213069 original size:20 final size:20
Alignment explanation
Indices: 1213044--1213086 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1213034 TCTAAGATCT
* *
1213044 CATTTAGGACCATGTAGATG
1 CATTTAGGAACATATAGATG
*
1213064 CATTTAGGAACATATAGTTG
1 CATTTAGGAACATATAGATG
1213084 CAT
1 CAT
1213087 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGAACATATAGATG
Found at i:1213463 original size:18 final size:18
Alignment explanation
Indices: 1213440--1213483 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
1213430 TTTCCAAATG
1213440 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
1213458 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
*
1213476 CCAATGCT
1 CCCATGCT
1213484 CACGAGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.43, G:0.20, T:0.18
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Found at i:1217367 original size:47 final size:47
Alignment explanation
Indices: 1217297--1217444 Score: 228
Period size: 47 Copynumber: 3.2 Consensus size: 47
1217287 TATAAAATCT
* * *
1217297 CTTACCATTT--ATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1217342 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
* *
1217389 CTTACCATTTAAATTCTATAAGCTTGTAAGCTTATTTTTCCAATATA
1 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
*
1217436 CTTGCCATT
1 CTTACCATT
1217445 ATTCTGTAAG
Statistics
Matches: 95, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
45 10 0.11
47 85 0.89
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.41
Consensus pattern (47 bp):
CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
Found at i:1217618 original size:40 final size:40
Alignment explanation
Indices: 1217574--1217775 Score: 395
Period size: 40 Copynumber: 5.0 Consensus size: 40
1217564 ACCGTAGTGG
1217574 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
1217614 TACACATAAGGTCGTGCCCATCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1217654 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1217694 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1217734 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1217774 TA
1 TA
1217776 TAAACCTACA
Statistics
Matches: 160, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 160 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:1226193 original size:16 final size:17
Alignment explanation
Indices: 1226172--1226205 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
1226162 ACTATTCACA
*
1226172 TGAATAGT-GAATTTTG
1 TGAATAGTAAAATTTTG
1226188 TGAATAGTAAAATTTTG
1 TGAATAGTAAAATTTTG
1226205 T
1 T
1226206 CGGCGATACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TGAATAGTAAAATTTTG
Found at i:1232710 original size:138 final size:138
Alignment explanation
Indices: 1232462--1232737 Score: 552
Period size: 138 Copynumber: 2.0 Consensus size: 138
1232452 CCGAAAAAGG
1232462 AATTTGGAGTAATATCCATATGGTAAACCTGACAACCTAATCCAAACAATTATCTGCGAAGGATG
1 AATTTGGAGTAATATCCATATGGTAAACCTGACAACCTAATCCAAACAATTATCTGCGAAGGATG
1232527 ATCATCTGATGTACTGAAATTCCTCGACCAAGGTTGAACTATTAAGTAATTCCCAAAAATTATCC
66 ATCATCTGATGTACTGAAATTCCTCGACCAAGGTTGAACTATTAAGTAATTCCCAAAAATTATCC
1232592 ATGGCCCC
131 ATGGCCCC
1232600 AATTTGGAGTAATATCCATATGGTAAACCTGACAACCTAATCCAAACAATTATCTGCGAAGGATG
1 AATTTGGAGTAATATCCATATGGTAAACCTGACAACCTAATCCAAACAATTATCTGCGAAGGATG
1232665 ATCATCTGATGTACTGAAATTCCTCGACCAAGGTTGAACTATTAAGTAATTCCCAAAAATTATCC
66 ATCATCTGATGTACTGAAATTCCTCGACCAAGGTTGAACTATTAAGTAATTCCCAAAAATTATCC
1232730 ATGGCCCC
131 ATGGCCCC
1232738 TCCGTCGAGA
Statistics
Matches: 138, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 138 1.00
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.28
Consensus pattern (138 bp):
AATTTGGAGTAATATCCATATGGTAAACCTGACAACCTAATCCAAACAATTATCTGCGAAGGATG
ATCATCTGATGTACTGAAATTCCTCGACCAAGGTTGAACTATTAAGTAATTCCCAAAAATTATCC
ATGGCCCC
Found at i:1238088 original size:72 final size:74
Alignment explanation
Indices: 1238003--1238214 Score: 295
Period size: 75 Copynumber: 2.9 Consensus size: 74
1237993 TATAGATGGC
* * *
1238003 GATCAGAATGATTGTGGCATGCATGATGCCAAGGTTTTAAGAAGCAGAAAGCATCCTATTAGGAA
1 GATCAAAATGATTGTAGCATGCATGATGCCAAGGTTTTAAGAAGCGGAAAGCATCCTATTAGGAA
1238068 -G-GTAGAT
66 GGCGTAGAT
* * * *
1238075 GATCAAAATGATTGTAGCATGCTTGATGTCAAGGTTTTAAGAAGCGGAAAGCAGCCTAAT-GGAA
1 GATCAAAATGATTGTAGCATGCATGATGCCAAGGTTTTAAGAAGCGGAAAGCATCCTATTAGG-A
* *
1238139 AGGTCGTTGGT
65 AGG-CGTAGAT
*
1238150 GATCAAAATGATTGTAGCATGCATGATGCAAAGGTTTTAAGAAGCGGAAAGCATCCTATTAGGAA
1 GATCAAAATGATTGTAGCATGCATGATGCCAAGGTTTTAAGAAGCGGAAAGCATCCTATTAGGAA
1238215 AGTTGTTCCT
Statistics
Matches: 121, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
71 2 0.02
72 55 0.45
73 1 0.01
75 61 0.50
76 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.25
Consensus pattern (74 bp):
GATCAAAATGATTGTAGCATGCATGATGCCAAGGTTTTAAGAAGCGGAAAGCATCCTATTAGGAA
GGCGTAGAT
Found at i:1242091 original size:21 final size:21
Alignment explanation
Indices: 1242067--1242115 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1242057 AACAAGGGAA
1242067 CTAATCCAGGATTGAGATGTT
1 CTAATCCAGGATTGAGATGTT
*
1242088 CTAATCCAGGATTGTGATGTT
1 CTAATCCAGGATTGAGATGTT
1242109 CTAATCC
1 CTAATCC
1242116 GCCTTAAAGG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (21 bp):
CTAATCCAGGATTGAGATGTT
Found at i:1242846 original size:17 final size:19
Alignment explanation
Indices: 1242814--1242849 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
1242804 TTTGTTATAG
1242814 TATTATCTTGTTTCTTTAT
1 TATTATCTTGTTTCTTTAT
1242833 TATTAT-TT-TTTCTTTAT
1 TATTATCTTGTTTCTTTAT
1242850 GGATTTATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 2 0.12
19 6 0.35
ACGTcount: A:0.17, C:0.08, G:0.03, T:0.72
Consensus pattern (19 bp):
TATTATCTTGTTTCTTTAT
Found at i:1249676 original size:157 final size:154
Alignment explanation
Indices: 1249448--1249758 Score: 570
Period size: 157 Copynumber: 2.0 Consensus size: 154
1249438 GTATTGTTGG
*
1249448 GGGAGCAGCAGCTATCGAAATGGGGGTTCCTCAGCGATGATCAAGGGAGCGAGTACGAAGAAATC
1 GGGAGCAGCAGCTATCGAAATGGGGGTTCCTCAGCGATGATAAAGGGAGCGAGTACGAAGAAATC
1249513 AGTGCAGGGGATTACCATTTATGTGGTTTGAGGAAGCCTTTAACCGGAAAGCACAG-AACTATGC
66 AGTGCAGGGGATTACCATTTATGTGGTTTGAGGAAGCCTTTAACCGGAAAGCACAGAAACTATGC
1249577 TTTTGTAGATTGTTGGGGTTATAA
131 TTTTGTAGATTGTTGGGGTTATAA
1249601 GGGAGCAGCAGCTATATCGAAATGGGGGTTCCTCAGCCGATGATAAAGGGAGCCGAGTACGAAGA
1 GGGAGCAGCAGC--TATCGAAATGGGGGTTCCTCAG-CGATGATAAAGGGAG-CGAGTACGAAGA
1249666 AATCAGTGCAGGGGATTACCATTTATGTGGTTTGAGGAAGCCTTTAACCGGAAAGCACAGAAACT
62 AATCAGTGCAGGGGATTACCATTTATGTGGTTTGAGGAAGCCTTTAACCGGAAAGCACAGAAACT
1249731 ATGCTTTTGTAGATTGTTGGGGTTATAA
127 ATGCTTTTGTAGATTGTTGGGGTTATAA
1249759 TATGACCAAG
Statistics
Matches: 152, Mismatches: 1, Indels: 5
0.96 0.01 0.03
Matches are distributed among these distances:
153 12 0.08
155 22 0.14
156 14 0.09
157 72 0.47
158 32 0.21
ACGTcount: A:0.29, C:0.15, G:0.31, T:0.25
Consensus pattern (154 bp):
GGGAGCAGCAGCTATCGAAATGGGGGTTCCTCAGCGATGATAAAGGGAGCGAGTACGAAGAAATC
AGTGCAGGGGATTACCATTTATGTGGTTTGAGGAAGCCTTTAACCGGAAAGCACAGAAACTATGC
TTTTGTAGATTGTTGGGGTTATAA
Found at i:1254146 original size:35 final size:36
Alignment explanation
Indices: 1254107--1254180 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
1254097 ATTTTCGGGA
* *
1254107 TTTGCTA-TTTTGGTAAAATTCGAATAAATACGATT
1 TTTGCTATTTTTGGCAAAATTCGAATAAAGACGATT
1254142 TTTGCTATTTTTGGCAAAATTCGAATAAAGACGATT
1 TTTGCTATTTTTGGCAAAATTCGAATAAAGACGATT
1254178 TTT
1 TTT
1254181 TTTTGCTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 7 0.19
36 29 0.81
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.43
Consensus pattern (36 bp):
TTTGCTATTTTTGGCAAAATTCGAATAAAGACGATT
Found at i:1259099 original size:35 final size:35
Alignment explanation
Indices: 1259056--1259129 Score: 139
Period size: 35 Copynumber: 2.1 Consensus size: 35
1259046 ATTTTCGGGA
*
1259056 TTTTGCTATTTTGGCAAAATTCGAATAAATACGAT
1 TTTTGCTATTTTGGCAAAATTCGAATAAAGACGAT
1259091 TTTTGCTATTTTGGCAAAATTCGAATAAAGACGAT
1 TTTTGCTATTTTGGCAAAATTCGAATAAAGACGAT
1259126 TTTT
1 TTTT
1259130 TTTGCTATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.42
Consensus pattern (35 bp):
TTTTGCTATTTTGGCAAAATTCGAATAAAGACGAT
Found at i:1267452 original size:24 final size:24
Alignment explanation
Indices: 1267425--1267486 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
1267415 CGTTCGTGAA
*
1267425 CGTTTGGTTATGTTCGTTTATATG
1 CGTTTAGTTATGTTCGTTTATATG
* *
1267449 CGTTTATTTATGTTCGTTTATGTG
1 CGTTTAGTTATGTTCGTTTATATG
* *
1267473 CGTTCATTTATGTT
1 CGTTTAGTTATGTT
1267487 TAACCTAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.13, C:0.10, G:0.21, T:0.56
Consensus pattern (24 bp):
CGTTTAGTTATGTTCGTTTATATG
Found at i:1267765 original size:33 final size:33
Alignment explanation
Indices: 1267720--1267809 Score: 162
Period size: 33 Copynumber: 2.7 Consensus size: 33
1267710 ATTTTCATTT
1267720 CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
1 CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
*
1267753 CTTCAACGATTCGACGGAGCTTCAAGTCTTCAA
1 CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
*
1267786 CTGCAACGATTCGACAGAGCTTCA
1 CTGCAACGATTCGACGGAGCTTCA
1267810 TCTCTTTCCC
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (33 bp):
CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
Found at i:1268294 original size:48 final size:48
Alignment explanation
Indices: 1268223--1268315 Score: 168
Period size: 48 Copynumber: 1.9 Consensus size: 48
1268213 GGGAAAGATG
*
1268223 AAGACTGTGGAATGGGTTGAATAGATGAACATGAACTGATGTTGGCTA
1 AAGACTGTGGAATGGGTTGAATAGATGAACATGAACTGATATTGGCTA
*
1268271 AAGACTGTGGACTGGGTTGAATAGATGAACATGAACTGATATTGG
1 AAGACTGTGGAATGGGTTGAATAGATGAACATGAACTGATATTGG
1268316 TCGAAGCCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.33, C:0.09, G:0.31, T:0.27
Consensus pattern (48 bp):
AAGACTGTGGAATGGGTTGAATAGATGAACATGAACTGATATTGGCTA
Found at i:1268308 original size:24 final size:24
Alignment explanation
Indices: 1268235--1268308 Score: 62
Period size: 24 Copynumber: 3.1 Consensus size: 24
1268225 GACTGTGGAA
1268235 TGGGTTGAATAGATGAACATGAAC
1 TGGGTTGAATAGATGAACATGAAC
* ** * * *
1268259 TGATGTTGGCTA-AAG-ACTGTGGAC
1 TG-GGTTGAATAGATGAAC-ATGAAC
1268283 TGGGTTGAATAGATGAACATGAAC
1 TGGGTTGAATAGATGAACATGAAC
1268307 TG
1 TG
1268309 ATATTGGTCG
Statistics
Matches: 34, Mismatches: 12, Indels: 8
0.63 0.22 0.15
Matches are distributed among these distances:
23 8 0.24
24 18 0.53
25 8 0.24
ACGTcount: A:0.32, C:0.09, G:0.31, T:0.27
Consensus pattern (24 bp):
TGGGTTGAATAGATGAACATGAAC
Found at i:1269020 original size:69 final size:67
Alignment explanation
Indices: 1268911--1269046 Score: 254
Period size: 69 Copynumber: 2.0 Consensus size: 67
1268901 CTGAAGTGAT
1268911 ATAAACCCAGAAAAGAATACTAGTATTGATGATAGCCTAATCAAGGTTGGAAAACATGAAACTGC
1 ATAAACCCAGAAAAGAATACTAGTATTGATGATAGCCTAATCAAGGTTGGAAAACATGAAACTGC
1268976 CC
66 CC
1268978 ATAAACCCAGAAAAGAATATACTAGTATTGATGATAGCCTAATCAAGGTTGGAAAACATGAAACT
1 ATAAACCCAGAAAAG-A-ATACTAGTATTGATGATAGCCTAATCAAGGTTGGAAAACATGAAACT
1269043 GCCC
64 GCCC
1269047 TGCCCTGTCA
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
67 15 0.22
68 1 0.01
69 51 0.76
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.21
Consensus pattern (67 bp):
ATAAACCCAGAAAAGAATACTAGTATTGATGATAGCCTAATCAAGGTTGGAAAACATGAAACTGC
CC
Found at i:1272512 original size:16 final size:16
Alignment explanation
Indices: 1272487--1272551 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
1272477 CCAACGTTTA
1272487 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1272503 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
1272519 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
*
1272535 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1272551 T
1 T
1272552 TTATTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.08, C:0.09, G:0.23, T:0.60
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1272914 original size:17 final size:18
Alignment explanation
Indices: 1272889--1272922 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1272879 TATAAGTTTC
1272889 TTTTCTAAAT-TATTTTA
1 TTTTCTAAATATATTTTA
*
1272906 TTTTTTAAATATATTTT
1 TTTTCTAAATATATTTT
1272923 TAATATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTCTAAATATATTTTA
Found at i:1272984 original size:28 final size:28
Alignment explanation
Indices: 1272951--1273007 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
1272941 TTAAAACGTA
1272951 TATAATGATATCAATTCAAAGAACGCCT
1 TATAATGATATCAATTCAAAGAACGCCT
*
1272979 TATAATGATATCAATTCGAAGAACGCCT
1 TATAATGATATCAATTCAAAGAACGCCT
1273007 T
1 T
1273008 CTTTAGTAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.30
Consensus pattern (28 bp):
TATAATGATATCAATTCAAAGAACGCCT
Found at i:1281456 original size:27 final size:27
Alignment explanation
Indices: 1281420--1281483 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
1281410 TACCCTAGCT
1281420 CATT-TAGCTTCAAAACCATCCCAAAG
1 CATTCTAGCTTCAAAACCATCCCAAAG
1281446 CATTCTAGCTTCAAAACCATCCCAAAG
1 CATTCTAGCTTCAAAACCATCCCAAAG
1281473 CATTCTAGCTT
1 CATTCTAGCTT
1281484 TCTTCCAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 4 0.11
27 33 0.89
ACGTcount: A:0.34, C:0.31, G:0.08, T:0.27
Consensus pattern (27 bp):
CATTCTAGCTTCAAAACCATCCCAAAG
Found at i:1296876 original size:18 final size:18
Alignment explanation
Indices: 1296855--1296889 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1296845 AAAAGAGTAA
1296855 TATTTTTATA-CTAATTAT
1 TATTTTTA-ACCTAATTAT
1296873 TATTTTTAACCTAATTA
1 TATTTTTAACCTAATTA
1296890 AATAAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.06
18 15 0.94
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTTAACCTAATTAT
Found at i:1297852 original size:46 final size:48
Alignment explanation
Indices: 1297809--1297902 Score: 120
Period size: 48 Copynumber: 2.0 Consensus size: 48
1297799 GACATTTACT
* *
1297809 TTATATTAACAT-ATATATA-TATATATATGAATAATATCAATTTAAA
1 TTATATTAACATAAAATATATTATATATATAAATAATATCAATTTAAA
** * *
1297855 TTATATTAATTTAAAATTTATTATATATATAAATTATATCAATTTAAA
1 TTATATTAACATAAAATATATTATATATATAAATAATATCAATTTAAA
1297903 ATATTACAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
46 10 0.25
47 5 0.12
48 25 0.62
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (48 bp):
TTATATTAACATAAAATATATTATATATATAAATAATATCAATTTAAA
Found at i:1297860 original size:15 final size:15
Alignment explanation
Indices: 1297842--1297902 Score: 61
Period size: 15 Copynumber: 3.9 Consensus size: 15
1297832 TATATGAATA
1297842 ATATCAATTTAAATT
1 ATATCAATTTAAATT
*
1297857 ATATTAATTTAAAATTT
1 ATATCAATTT-AAA-TT
*
1297874 ATTAT-ATATATAAATT
1 A-TATCA-ATTTAAATT
1297890 ATATCAATTTAAA
1 ATATCAATTTAAA
1297903 ATATTACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
15 18 0.47
16 7 0.18
17 7 0.18
18 6 0.16
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
ATATCAATTTAAATT
Found at i:1297888 original size:17 final size:17
Alignment explanation
Indices: 1297809--1297893 Score: 58
Period size: 15 Copynumber: 5.4 Consensus size: 17
1297799 GACATTTACT
* *
1297809 TTATATTAACATATATA
1 TTATATTAATATATAAA
*
1297826 -TATA-T-ATATATGAA
1 TTATATTAATATATAAA
* *
1297840 TAATATCAAT-T-TAAA
1 TTATATTAATATATAAA
*
1297855 TTATATTAATTTA-AAA
1 TTATATTAATATATAAA
1297871 TT-TATTATATATATAAA
1 TTATATTA-ATATATAAA
1297888 TTATAT
1 TTATAT
1297894 CAATTTAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 15
0.68 0.12 0.20
Matches are distributed among these distances:
14 6 0.12
15 20 0.39
16 15 0.29
17 7 0.14
18 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.48
Consensus pattern (17 bp):
TTATATTAATATATAAA
Found at i:1297927 original size:48 final size:46
Alignment explanation
Indices: 1297828--1297919 Score: 116
Period size: 48 Copynumber: 2.0 Consensus size: 46
1297818 CATATATATA
* *
1297828 TATATATATGAATAATATCAATTTAAATTATATTAATTTAAAATTTAT
1 TATATATATAAATAATATCAATTTAAA-TATATTAA-TAAAAATTTAT
*
1297876 TATATATATAAATTATATCAATTTAAA-ATATTACA-AAAAATTTA
1 TATATATATAAATAATATCAATTTAAATATATTA-ATAAAAATTTA
1297920 AAATTATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
45 8 0.20
46 6 0.15
47 1 0.03
48 25 0.62
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (46 bp):
TATATATATAAATAATATCAATTTAAATATATTAATAAAAATTTAT
Found at i:1298224 original size:229 final size:228
Alignment explanation
Indices: 1297766--1298224 Score: 590
Period size: 230 Copynumber: 2.0 Consensus size: 228
1297756 AAAAAATATC
* *
1297766 TATTAGAGATTTTATGTTATAAATTAAAAATATGACATTTACTTTATATTAACATATATATATAT
1 TATTAGAGATTTTATGTTATAAATTAAAAATATAACATTTACATTATATTAACATATATATATAT
*
1297831 ATATATGAATAATATCAATTTAAATTATATTAATTTAAAATTTATTATATATATAAATTATATCA
66 ATATAT-AATAATATCAATTTAAATTATAATAATTTAAAATTTATTATATATATAAATTATATCA
* * *
1297896 ATTTAAAATATTACAAAAAATTTAAAATTATAATTATAATAAAAATATATTTTATATAACTCTAT
130 ATTTAAAATATAACAAAAAAATTAAAA-TATAATCATAATAAAAATATATTTTATATAACTCTAT
* * *
1297961 ATTAATATTTTAATGTGTAAAACATAAACTTTATT
194 ATTAATACTGTAATGTATAAAACATAAACTTTATT
* ** *
1297996 TATTAGAGATTTTATGTTGTAAATTAAAAATATAACATTTACATTATATTTTCACT-TTTATATA
1 TATTAGAGATTTTATGTTATAAATTAAAAATATAACATTTACATTATATTAACA-TATATATATA
* * * *
1298060 TATATAT-ATAATGTCTATTTAAATTTTAATAATTTTAAAAAAATTATTATTATATGTATAAATT
65 TATATATAATAATATCAATTTAAATTATAATAA-TTT---AAAA-T-TTATTATATATATAAATT
*
1298124 ATATCAATTTAAACTATAACAAACAAAATT-AAA-AT-A-CA-AATAAAAATATATTTTATATAA
124 ATATCAATTTAAAATATAACAAA-AAAATTAAAATATAATCATAATAAAAATATATTTTATATAA
* **
1298184 CTCTCTATTAATACTGTAATGTATAAATTATAAACTTTATT
188 CTCTATATTAATACTGTAATGTATAAAACATAAACTTTATT
1298225 AATTTTTAAA
Statistics
Matches: 200, Mismatches: 21, Indels: 17
0.84 0.09 0.07
Matches are distributed among these distances:
228 21 0.10
229 60 0.30
230 64 0.32
231 2 0.01
232 6 0.03
233 1 0.00
234 41 0.20
235 5 0.03
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.44
Consensus pattern (228 bp):
TATTAGAGATTTTATGTTATAAATTAAAAATATAACATTTACATTATATTAACATATATATATAT
ATATATAATAATATCAATTTAAATTATAATAATTTAAAATTTATTATATATATAAATTATATCAA
TTTAAAATATAACAAAAAAATTAAAATATAATCATAATAAAAATATATTTTATATAACTCTATAT
TAATACTGTAATGTATAAAACATAAACTTTATT
Found at i:1298250 original size:229 final size:227
Alignment explanation
Indices: 1297784--1298250 Score: 509
Period size: 229 Copynumber: 2.0 Consensus size: 227
1297774 ATTTTATGTT
* *
1297784 ATAAATTAAAAATATGACATTTACTTTATATTAACATATATATATATATATATGAATAATATCAA
1 ATAAATTAAAAATATAACATTTACATTATATTAACATATATATATATATATAT-AATAATATCAA
* *
1297849 TTTAAATTATATTAATTTAAAATTTATTATATATATAAATTATATCAATTTAAAATATTACAAAA
65 TTTAAATTATAATAATTTAAAATTTATTATATATATAAATTATATCAATTTAAAATATAACAAAA
* * * * *
1297914 AATTTAAAATTATAATTATAATAAAAATATATTTTATATAACTCTATATTAATATTTTAATGTGT
130 AAATTAAAA-TATAATCATAATAAAAATATATTTTATATAACTCTATATTAATACTGTAATGTAT
* * * **
1297979 AAAACATAAACTTTATTTATTAGAGATTTTATGTT
194 AAAACATAAACTTTATTAATTAGAAATATTA-GAA
* ** * * *
1298014 GTAAATTAAAAATATAACATTTACATTATATTTTCACT-TTTATATATATATAT-ATAATGTCTA
1 ATAAATTAAAAATATAACATTTACATTATATTAACA-TATATATATATATATATAATAATATCAA
* * *
1298077 TTTAAATTTTAATAATTTTAAAAAAATTATTATTATATGTATAAATTATATCAATTTAAACTATA
65 TTTAAATTATAATAA-TTT---AAAA-T-TTATTATATATATAAATTATATCAATTTAAAATATA
*
1298142 ACAAACAAAATT-AAA-AT-A-CA-AATAAAAATATATTTTATATAACTCTCTATTAATACTGTA
124 ACAAA-AAAATTAAAATATAATCATAATAAAAATATATTTTATATAACTCTATATTAATACTGTA
** **
1298202 ATGTATAAATTATAAACTTTATTAATTTTTAAATGATTA-AA
188 ATGTATAAAACATAAACTTTATTAA-TTAGAAAT-ATTAGAA
1298243 ATAAATTA
1 ATAAATTA
1298251 TTAAAAGTAA
Statistics
Matches: 198, Mismatches: 29, Indels: 21
0.80 0.12 0.08
Matches are distributed among these distances:
228 21 0.11
229 68 0.34
230 51 0.26
231 5 0.03
232 6 0.03
233 1 0.01
234 41 0.21
235 5 0.03
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (227 bp):
ATAAATTAAAAATATAACATTTACATTATATTAACATATATATATATATATATAATAATATCAAT
TTAAATTATAATAATTTAAAATTTATTATATATATAAATTATATCAATTTAAAATATAACAAAAA
AATTAAAATATAATCATAATAAAAATATATTTTATATAACTCTATATTAATACTGTAATGTATAA
AACATAAACTTTATTAATTAGAAATATTAGAA
Found at i:1300350 original size:20 final size:20
Alignment explanation
Indices: 1300304--1300351 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
1300294 TACGTATTTT
* *
1300304 ATTATTATTTTAAATAATTT
1 ATTATTATTATAAATAATTG
*
1300324 ATGATTATTATAAGAT-ATTG
1 ATTATTATTATAA-ATAATTG
1300344 ATTATTAT
1 ATTATTAT
1300352 AAGATATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (20 bp):
ATTATTATTATAAATAATTG
Found at i:1300366 original size:17 final size:17
Alignment explanation
Indices: 1300325--1300359 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1300315 AAATAATTTA
1300325 TGATTATTATAAGATAT
1 TGATTATTATAAGATAT
1300342 TGATTATTATAAGATAT
1 TGATTATTATAAGATAT
1300359 T
1 T
1300360 ATATATTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (17 bp):
TGATTATTATAAGATAT
Found at i:1300817 original size:25 final size:24
Alignment explanation
Indices: 1300769--1300818 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1300759 AATCCCCGCG
* *
1300769 ATTTTTTAAGCGGGACGGATACGA
1 ATTTTTTAAACGGGACGGAGACGA
*
1300793 ATTTTTTAAACGGGAACGGGGACGA
1 ATTTTTTAAACGGG-ACGGAGACGA
1300818 A
1 A
1300819 GAACCAATAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.32, C:0.12, G:0.30, T:0.26
Consensus pattern (24 bp):
ATTTTTTAAACGGGACGGAGACGA
Found at i:1301937 original size:2 final size:2
Alignment explanation
Indices: 1301930--1301961 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1301920 TGTGTACTTA
1301930 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
1301962 TTTTAAATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1304016 original size:25 final size:24
Alignment explanation
Indices: 1303973--1304022 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
1303963 GAAAAAATAT
1303973 AAAATAAAGAATGAAATTAATTAAA
1 AAAATAAAGAATGAAATTAA-TAAA
*
1303998 AAAATAAATAAT-AATATTAATAAA
1 AAAATAAAGAATGAA-ATTAATAAA
1304022 A
1 A
1304023 TATTTTCCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 7 0.30
25 16 0.70
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (24 bp):
AAAATAAAGAATGAAATTAATAAA
Found at i:1304111 original size:28 final size:29
Alignment explanation
Indices: 1304075--1304130 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
1304065 ATTATAAATT
*
1304075 TTTTGAAAAATG-TTTCAAAACTATATAG
1 TTTTCAAAAATGTTTTCAAAACTATATAG
*
1304103 TTTTCAAAAATGTTTTTAAAACTATATA
1 TTTTCAAAAATGTTTTCAAAACTATATA
1304131 CTATATAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (29 bp):
TTTTCAAAAATGTTTTCAAAACTATATAG
Found at i:1304134 original size:36 final size:35
Alignment explanation
Indices: 1304093--1304182 Score: 121
Period size: 36 Copynumber: 2.5 Consensus size: 35
1304083 AATGTTTCAA
* *
1304093 AACTATATAGTTTTCAAAAATGTTTTTAAAACTAT
1 AACTATATAGTTTTCAAAAATGATTTCAAAACTAT
1304128 ATACTATATAAGTTTTC-AAAATGATTTCAAAACTAT
1 A-ACTATAT-AGTTTTCAAAAATGATTTCAAAACTAT
1304164 AA-TATATATGTTTTCAAAA
1 AACTATATA-GTTTTCAAAA
1304183 GAGAAAATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
33 1 0.02
34 11 0.22
35 5 0.10
36 25 0.51
37 7 0.14
ACGTcount: A:0.44, C:0.09, G:0.06, T:0.41
Consensus pattern (35 bp):
AACTATATAGTTTTCAAAAATGATTTCAAAACTAT
Found at i:1304340 original size:20 final size:20
Alignment explanation
Indices: 1304315--1304408 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
1304305 CTATCGCAAA
1304315 TTCGCGTTGCGATTTTCCAT
1 TTCGCGTTGCGATTTTCCAT
*
1304335 TTCGCGTTGCGATTTTCCAG
1 TTCGCGTTGCGATTTTCCAT
* ** *
1304355 TTCGCGTTGCGATAGTTGAAA
1 TTCGCGTTGCGAT-TTTCCAT
* *
1304376 ATCGCGTTGCGATTTTTCAT
1 TTCGCGTTGCGATTTTCCAT
1304396 TTCGCGTTGCGAT
1 TTCGCGTTGCGAT
1304409 AGTCTACAGT
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.40
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCCAT
Found at i:1304451 original size:63 final size:63
Alignment explanation
Indices: 1304323--1304474 Score: 211
Period size: 63 Copynumber: 2.4 Consensus size: 63
1304313 AATTCGCGTT
* * * ***
1304323 GCGATTTTCCATTTCGCGTTGCGAT--TTTCCAGTTCGCGTTGCGATAGTTGAAAATCGCGTT
1 GCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTCGCGTTGCGATAGTTGAAAATCACAAC
*
1304384 GCGATTTTTCATTTCGCGTTGCGATAGTCTACAGTT-GTCGTTGCGATAGTTGAAAATCACAAC
1 GCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTCG-CGTTGCGATAGTTGAAAATCACAAC
1304447 GCGATTTTCCATTTCGCGTTGCGATAGT
1 GCGATTTTCCATTTCGCGTTGCGATAGT
1304475 TGAAAATCGC
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
61 24 0.30
62 1 0.01
63 55 0.69
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (63 bp):
GCGATTTTCCATTTCGCGTTGCGATAGTCTACAGTTCGCGTTGCGATAGTTGAAAATCACAAC
Found at i:1304471 original size:41 final size:40
Alignment explanation
Indices: 1304422--1304511 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 40
1304412 CTACAGTTGT
*
1304422 CGTTGCGATAGTTGAAAATCACAACGCGATTTTCCATTTCG
1 CGTTGCGATAGTTGAAAATCACAAAGCGATTTTCCATTT-G
*
1304463 CGTTGCGATAGTTGAAAATCGCAAAGCGATTTTCCATTTG
1 CGTTGCGATAGTTGAAAATCACAAAGCGATTTTCCATTTG
*
1304503 TGTTGCGAT
1 CGTTGCGAT
1304512 TTTCCATTTC
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
40 9 0.20
41 37 0.80
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (40 bp):
CGTTGCGATAGTTGAAAATCACAAAGCGATTTTCCATTTG
Found at i:1304512 original size:19 final size:20
Alignment explanation
Indices: 1304488--1304531 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
1304478 AAATCGCAAA
1304488 GCGATTTTCCATTT-GTGTT
1 GCGATTTTCCATTTCGTGTT
1304507 GCGATTTTCCATTTCGTGTT
1 GCGATTTTCCATTTCGTGTT
1304527 GCGAT
1 GCGAT
1304532 AGTCTACAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.11, C:0.18, G:0.23, T:0.48
Consensus pattern (20 bp):
GCGATTTTCCATTTCGTGTT
Found at i:1304551 original size:22 final size:22
Alignment explanation
Indices: 1304523--1304575 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1304513 TTCCATTTCG
1304523 TGTTGCGATAGTCTACAGTTGT
1 TGTTGCGATAGTCTACAGTTGT
1304545 TGTTGCGATAGTCTACAGTTGT
1 TGTTGCGATAGTCTACAGTTGT
*
1304567 CGTTGCGAT
1 TGTTGCGAT
1304576 TTTCCAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.40
Consensus pattern (22 bp):
TGTTGCGATAGTCTACAGTTGT
Found at i:1305357 original size:22 final size:22
Alignment explanation
Indices: 1305329--1305381 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1305319 AATTTGGAAA
*
1305329 ATCGCAACGACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
1305351 ATCGCAACAACAACTGTAGACT
1 ATCGCAACAACAACTGTAGACT
1305373 ATCGCAACA
1 ATCGCAACA
1305382 CGAAATGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (22 bp):
ATCGCAACAACAACTGTAGACT
Found at i:1305421 original size:20 final size:20
Alignment explanation
Indices: 1305373--1305424 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1305363 ACTGTAGACT
*
1305373 ATCGCAACACGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1305393 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
1305413 ATCGCAACGCGA
1 ATCGCAACGCGA
1305425 TTTTCAACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:1305448 original size:39 final size:39
Alignment explanation
Indices: 1305393--1305481 Score: 142
Period size: 39 Copynumber: 2.2 Consensus size: 39
1305383 GAAATGGAAA
*
1305393 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAA--CGAAATGGAAAATCGCAACGCAATTTTCAACT
*
1305434 ATTGCAACGAAATGGAAAATCGCAACGCAATTTTCAACT
1 ATCGCAACGAAATGGAAAATCGCAACGCAATTTTCAACT
1305473 ATCGCAACG
1 ATCGCAACG
1305482 CGAAATGCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 39 0.87
41 6 0.13
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (39 bp):
ATCGCAACGAAATGGAAAATCGCAACGCAATTTTCAACT
Found at i:1305478 original size:21 final size:21
Alignment explanation
Indices: 1305413--1305482 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 21
1305403 GAAATGGAAA
*
1305413 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCAATTTTCAACT
* * ** *
1305434 ATTGCAACG-AA-ATGGAA-A
1 ATCGCAACGCAATTTTCAACT
1305452 ATCGCAACGCAATTTTCAACT
1 ATCGCAACGCAATTTTCAACT
1305473 ATCGCAACGC
1 ATCGCAACGC
1305483 GAAATGCATT
Statistics
Matches: 35, Mismatches: 11, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 8 0.23
19 5 0.14
20 4 0.11
21 18 0.51
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCAATTTTCAACT
Found at i:1305682 original size:30 final size:31
Alignment explanation
Indices: 1305629--1305686 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
1305619 TTATTTTCTC
1305629 TTTTCAAAATGTTTTTAAAAAACTATATTTA
1 TTTTCAAAATGTTTTTAAAAAACTATATTTA
1305660 TTTTCAAAATGTTTTT-AAAAACTATAT
1 TTTTCAAAATGTTTTTAAAAAACTATAT
1305687 AATATACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
30 11 0.41
31 16 0.59
ACGTcount: A:0.41, C:0.07, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTTCAAAATGTTTTTAAAAAACTATATTTA
Found at i:1305720 original size:34 final size:34
Alignment explanation
Indices: 1305672--1305760 Score: 108
Period size: 34 Copynumber: 2.6 Consensus size: 34
1305662 TTCAAAATGT
*
1305672 TTTTAAAAACTATATAATATACA-TTTTAAAACCG
1 TTTTAAAAACTATATAATATACATTTTTAAAA-CA
* * ** *
1305706 TTTTAAAAATTATATTATATTTATTTTTAAAATA
1 TTTTAAAAACTATATAATATACATTTTTAAAACA
1305740 TTTTAAAAACTATATAATATA
1 TTTTAAAAACTATATAATATA
1305761 TAAACATTTT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
34 37 0.82
35 8 0.18
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (34 bp):
TTTTAAAAACTATATAATATACATTTTTAAAACA
Found at i:1305788 original size:39 final size:39
Alignment explanation
Indices: 1305734--1305837 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 39
1305724 ATTTATTTTT
* *
1305734 AAAATATTTTAAAAACTATATAATATATAAACATTTTCA
1 AAAATGTTTTCAAAACTATATAATATATAAACATTTTCA
** * * * *
1305773 ATCATGTTTTCAAAACTATATATTATATATATATTTTTA
1 AAAATGTTTTCAAAACTATATAATATATAAACATTTTCA
1305812 AAAATGTTTTC-AAAC-A-ATAATATATA
1 AAAATGTTTTCAAAACTATATAATATATA
1305838 TATGTATGTA
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
36 9 0.17
37 1 0.02
38 4 0.07
39 40 0.74
ACGTcount: A:0.48, C:0.08, G:0.02, T:0.42
Consensus pattern (39 bp):
AAAATGTTTTCAAAACTATATAATATATAAACATTTTCA
Found at i:1306273 original size:20 final size:20
Alignment explanation
Indices: 1306241--1306314 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
1306231 TTTTCCCAAT
*
1306241 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
* ** *
1306261 TCACAACGCGAATTGGGAAAA
1 TCGCAACGCGAA-TAAGTAAA
*
1306282 TCGCAATGCGAATAAGTAAA
1 TCGCAACGCGAATAAGTAAA
1306302 TCGCAACGCGAAT
1 TCGCAACGCGAAT
1306315 TGGGAAAATC
Statistics
Matches: 42, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 27 0.64
21 15 0.36
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATAAGTAAA
Found at i:1306286 original size:41 final size:41
Alignment explanation
Indices: 1306241--1306330 Score: 171
Period size: 41 Copynumber: 2.2 Consensus size: 41
1306231 TTTTCCCAAT
1306241 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
*
1306282 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
1306323 TCGCAATG
1 TCGCAATG
1306331 TGATACTGAC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCACAACGCGAATTGGGAAAA
Found at i:1306292 original size:21 final size:20
Alignment explanation
Indices: 1306241--1306369 Score: 82
Period size: 20 Copynumber: 6.3 Consensus size: 20
1306231 TTTTCCCAAT
*
1306241 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* * **
1306261 TCACAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
*
1306282 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGAAAA
* **
1306302 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGAAAA
* * **
1306323 TCGCAATGTG-ATACTGACTA
1 TCGCAATGCGAATA-AGAAAA
1306343 TCGCAATGCGATAATAA-AAAA
1 TCGCAATGCG--AATAAGAAAA
1306364 TCGCAA
1 TCGCAA
1306370 CGAGATACTT
Statistics
Matches: 79, Mismatches: 24, Indels: 11
0.69 0.21 0.10
Matches are distributed among these distances:
19 1 0.01
20 39 0.49
21 36 0.46
23 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGAAAA
Found at i:1306346 original size:41 final size:41
Alignment explanation
Indices: 1306264--1306394 Score: 115
Period size: 41 Copynumber: 3.2 Consensus size: 41
1306254 AAGTAAATCA
* * *
1306264 CAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-AATCG
1 CAACGCGAATTGGGAAAATCGCAATGAG-ATACTG-ACTATCG
*
1306305 CAACGCGAATTGGGAAAATCGCAATGTGATACTGACTATCG
1 CAACGCGAATTGGGAAAATCGCAATGAGATACTGACTATCG
* * ** * * *
1306346 CAATGCGATAAT-AAAAAATCGCAACGAGATACTTACTTTCG
1 CAACGCGA-ATTGGGAAAATCGCAATGAGATACTGACTATCG
1306387 CAACGCGA
1 CAACGCGA
1306395 TACTGACTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
40 4 0.05
41 69 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.20
Consensus pattern (41 bp):
CAACGCGAATTGGGAAAATCGCAATGAGATACTGACTATCG
Found at i:1306389 original size:20 final size:20
Alignment explanation
Indices: 1306364--1306416 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
1306354 TAATAAAAAA
* *
1306364 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
1306384 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
1306404 TCGCAACGCGATA
1 TCGCAACGCGATA
1306417 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:1306946 original size:20 final size:20
Alignment explanation
Indices: 1306923--1306965 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
1306913 GATAGTCGAA
1306923 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
1306943 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
1306963 TTC
1 TTC
1306966 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:1308306 original size:18 final size:18
Alignment explanation
Indices: 1308285--1308329 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1308275 TTCACTTCGG
*
1308285 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1308303 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1308321 GAGCCATCA
1 GAGCCATCA
1308330 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1308863 original size:19 final size:20
Alignment explanation
Indices: 1308809--1308875 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
1308799 TAGTTTACTT
* *
1308809 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
1308829 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
1308849 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
1308868 TCGCAACG
1 TCGCAACG
1308876 ACAAAATGGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1308887 original size:14 final size:14
Alignment explanation
Indices: 1308864--1308921 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
1308854 ATGCGAAATG
1308864 AAAATCGCAACGAC
1 AAAATCGCAACGAC
* *
1308878 AAAATGGCAATGCGAA
1 AAAATCGCAA--CGAC
1308894 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
1308910 AAAATCGCAACG
1 AAAATCGCAACG
1308922 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
14 20 0.56
16 8 0.22
18 8 0.22
ACGTcount: A:0.48, C:0.22, G:0.19, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:1308906 original size:32 final size:32
Alignment explanation
Indices: 1308848--1308936 Score: 151
Period size: 32 Copynumber: 2.8 Consensus size: 32
1308838 GGAAATGGCT
1308848 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
*
1308881 ATGGCAATGCGAAATGAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAATCGCAACGACAAA
*
1308913 ATCGCAACGCGAAATGAAATCGCA
1 ATCGCAATGCGAAATGAAATCGCA
1308937 TGCGATTTGT
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 38 0.72
33 15 0.28
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.12
Consensus pattern (32 bp):
ATCGCAATGCGAAATGAAATCGCAACGACAAA
Found at i:1308985 original size:32 final size:33
Alignment explanation
Indices: 1308948--1309026 Score: 115
Period size: 32 Copynumber: 2.4 Consensus size: 33
1308938 GCGATTTGTG
**
1308948 TTTCGCGTTGCGATTTTGTCGTTACGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCAATACGATTTTCA
*
1308980 TTTCGCGTTGCGATTTTGTCAATGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCAATACGATTTTCA
*
1309013 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
1309027 AGCCATTTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 24 0.57
33 18 0.43
ACGTcount: A:0.14, C:0.19, G:0.22, T:0.46
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCAATACGATTTTCA
Found at i:1309026 original size:19 final size:20
Alignment explanation
Indices: 1309002--1309049 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
1308992 ATTTTGTCAA
1309002 TGCGATTTTCATTT-CGCAT
1 TGCGATTTTCATTTCCGCAT
*** *
1309021 TGCGATAGCCATTTCCGCGT
1 TGCGATTTTCATTTCCGCAT
1309041 TGCGATTTT
1 TGCGATTTT
1309050 AAGTTTCGTG
Statistics
Matches: 21, Mismatches: 7, Indels: 1
0.72 0.24 0.03
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (20 bp):
TGCGATTTTCATTTCCGCAT
Found at i:1310860 original size:14 final size:14
Alignment explanation
Indices: 1310841--1310876 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1310831 ATTGTTTAAT
1310841 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
1310855 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
1310869 TGATTTGT
1 TGATTTGT
1310877 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1311015 original size:19 final size:19
Alignment explanation
Indices: 1310993--1311060 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
1310983 ATCGCAACGA
1310993 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1311012 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1311031 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1311045 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1311061 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1312225 original size:24 final size:24
Alignment explanation
Indices: 1312174--1312227 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
1312164 GTATTCGAAA
* * *
1312174 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACAGAC
*
1312198 TTTGATATTGGTCAATACACAGAT
1 TTTGATATTGGTCAATACACAGAC
1312222 TTTGAT
1 TTTGAT
1312228 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACAGAC
Found at i:1314931 original size:13 final size:13
Alignment explanation
Indices: 1314913--1314972 Score: 50
Period size: 14 Copynumber: 4.5 Consensus size: 13
1314903 AATTATGTTA
1314913 AAATCAATTAAAC
1 AAATCAATTAAAC
**
1314926 AAATCAACTTTTAC
1 AAATCAA-TTAAAC
* **
1314940 AAATCACCTTTTAC
1 AAATCA-ATTAAAC
1314954 AAATCAATTAAAC
1 AAATCAATTAAAC
1314967 -AATCAA
1 AAATCAA
1314973 AAAATAAGCA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
12 6 0.15
13 11 0.28
14 22 0.56
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATCAATTAAAC
Found at i:1314943 original size:14 final size:14
Alignment explanation
Indices: 1314924--1314960 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1314914 AATCAATTAA
1314924 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1314938 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1314952 ACAAATCAA
1 ACAAATCAA
1314961 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1316373 original size:21 final size:21
Alignment explanation
Indices: 1316307--1316373 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1316297 GTGAATCGGG
*
1316307 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1316327 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1316349 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1316370 CTCT
1 CTCT
1316374 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1318510 original size:33 final size:33
Alignment explanation
Indices: 1318453--1318552 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 33
1318443 ACGAGGTAAT
* *
1318453 GAGAATCGCAACACGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
1318487 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
1318520 GACAATCGCAACGCGAAATGAAAATCGCAACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
1318553 CGAAATAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.41, C:0.26, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:1318558 original size:20 final size:19
Alignment explanation
Indices: 1318428--1318593 Score: 109
Period size: 20 Copynumber: 9.1 Consensus size: 19
1318418 TCTTTTGGTT
*
1318428 GAAATGAAAATCGCAACGAG
1 GAAATGAAAATCGCAACG-C
* * *
1318448 GTAATGAGAATCGCAACAC
1 GAAATGAAAATCGCAACGC
**
1318467 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1318485 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
1318501 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
1318519 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1318534 GAAATGAAAATCGCAACCAC
1 GAAATGAAAATCGCAA-CGC
*
1318554 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1318573 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1318592 GA
1 GA
1318594 TTTTTGTTTC
Statistics
Matches: 114, Mismatches: 20, Indels: 25
0.72 0.13 0.16
Matches are distributed among these distances:
14 19 0.17
15 3 0.03
16 2 0.02
17 1 0.01
18 4 0.04
19 40 0.35
20 45 0.39
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1318625 original size:19 final size:19
Alignment explanation
Indices: 1318589--1318655 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
1318579 AAAATCGCAA
*
1318589 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
1318608 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
**
1318627 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CGCGT
1318647 TGCGATTTT
1 TGCGATTTT
1318656 CATTCTCGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
19 28 0.70
20 12 0.30
ACGTcount: A:0.09, C:0.16, G:0.24, T:0.51
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:1319249 original size:20 final size:20
Alignment explanation
Indices: 1319164--1319277 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
1319154 CGCTATGTAA
* * *
1319164 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
*
1319184 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
1319204 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
1319225 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
1319245 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
1319265 ATCGCATTGCGAT
1 ATCGCATTGCGAT
1319278 TTTCCCAATT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 3 0.04
20 62 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:1319262 original size:61 final size:61
Alignment explanation
Indices: 1319164--1319280 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
1319154 CGCTATGTAA
* * * *
1319164 ATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
1319225 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
1319281 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:1319297 original size:61 final size:61
Alignment explanation
Indices: 1319164--1319298 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
1319154 CGCTATGTAA
* * * * ** *
1319164 ATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
1319225 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
*
1319287 -TCGCGCTGCGAT
1 ATCGCGTTGCGAT
1319299 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:1319388 original size:21 final size:21
Alignment explanation
Indices: 1319348--1319388 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1319338 ATTGTATACC
**
1319348 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
1319369 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
1319389 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:1320212 original size:16 final size:17
Alignment explanation
Indices: 1320180--1320227 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
1320170 AACTTTTTAT
*
1320180 GATTTTTAATAACTTAA
1 GATTTTTAATAAATTAA
1320197 GATTTTTAA-AAATTAA
1 GATTTTTAATAAATTAA
* *
1320213 AAGTTTTACATAAAT
1 GATTTTTA-ATAAAT
1320228 ATATTAACAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 12 0.46
17 10 0.38
18 4 0.15
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (17 bp):
GATTTTTAATAAATTAA
Found at i:1321721 original size:21 final size:21
Alignment explanation
Indices: 1321669--1321721 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1321659 GTTTCCAAAT
1321669 TCGCAACGCGAACATCGACGA
1 TCGCAACGCGAACATCGACGA
* * *
1321690 TCGTAACGCGAACTTCGACTA
1 TCGCAACGCGAACATCGACGA
*
1321711 TCGCAATGCGA
1 TCGCAACGCGA
1321722 TTTTCCAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.23, T:0.17
Consensus pattern (21 bp):
TCGCAACGCGAACATCGACGA
Found at i:1321741 original size:19 final size:19
Alignment explanation
Indices: 1321717--1321783 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 19
1321707 ACTATCGCAA
1321717 TGCGATTTTCCAAATTCGT
1 TGCGATTTTCCAAATTCGT
** *
1321736 TGCGATAGTCCAAGTTCGCGT
1 TGCGATTTTCCAAATT--CGT
1321757 TGCGATTTATTCCAAATTCGT
1 TGCGA-TT-TTCCAAATTCGT
1321778 TGCGAT
1 TGCGAT
1321784 AGTCCACGCG
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
19 13 0.34
20 1 0.03
21 16 0.42
22 1 0.03
23 7 0.18
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (19 bp):
TGCGATTTTCCAAATTCGT
Found at i:1321759 original size:21 final size:19
Alignment explanation
Indices: 1321725--1321789 Score: 76
Period size: 21 Copynumber: 3.2 Consensus size: 19
1321715 AATGCGATTT
1321725 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
* *
1321744 TCCAAGTTCGCGTTGCGATTTAT
1 TCCAAATT--CGTTGCGA--TAG
1321767 TCCAAATTCGTTGCGATAG
1 TCCAAATTCGTTGCGATAG
1321786 TCCA
1 TCCA
1321790 CGCGAACATC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
19 13 0.34
21 16 0.42
23 9 0.24
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.34
Consensus pattern (19 bp):
TCCAAATTCGTTGCGATAG
Found at i:1321868 original size:21 final size:21
Alignment explanation
Indices: 1321789--1321875 Score: 90
Period size: 21 Copynumber: 4.3 Consensus size: 21
1321779 GCGATAGTCC
* *
1321789 ACGCGAACATCGACGATCGCA
1 ACGCGAACTTCGACTATCGCA
*
1321810 ACGCGAACTTGGACTATCGCA
1 ACGCGAACTTCGACTATCGCA
* * *
1321831 A--CAAATTTGGA-TATCGCA
1 ACGCGAACTTCGACTATCGCA
1321849 ACGCGAACTTCGACTATCGCA
1 ACGCGAACTTCGACTATCGCA
*
1321870 ATGCGA
1 ACGCGA
1321876 TTTTCCAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
18 8 0.15
19 8 0.15
20 7 0.13
21 31 0.57
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (21 bp):
ACGCGAACTTCGACTATCGCA
Found at i:1322055 original size:38 final size:39
Alignment explanation
Indices: 1322005--1322083 Score: 126
Period size: 38 Copynumber: 2.1 Consensus size: 39
1321995 CAAATCGTGT
1322005 TTTTTCAAATAATTTAGAGTAATT-ATAAAGTATTATATG
1 TTTTTCAAATAATTTAGAGTAATTCA-AAAGTATTATATG
*
1322044 TTTTT-AAATAATTTGGAGTAATTCAAAAGTATTATATG
1 TTTTTCAAATAATTTAGAGTAATTCAAAAGTATTATATG
1322082 TT
1 TT
1322084 CAGAAGTTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
38 32 0.84
39 6 0.16
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (39 bp):
TTTTTCAAATAATTTAGAGTAATTCAAAAGTATTATATG
Found at i:1334192 original size:4 final size:4
Alignment explanation
Indices: 1334183--1334211 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1334173 TACCGTCTTC
1334183 ATTT ATTT ATTT ATTT ATTT A-TT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
1334212 GTTAGTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:1337375 original size:36 final size:37
Alignment explanation
Indices: 1337303--1337379 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
1337293 AATTAAATTT
* * * *
1337303 TAAAAAATAGATAAATAGGAGAGAGGGTTGGTCATCA
1 TAAAAAAAAGATAAACAGAAGAGAGGGTTGGACATCA
*
1337340 TAAAAAAAAGATAAACAGAAGGGAGGGTT-GACATCA
1 TAAAAAAAAGATAAACAGAAGAGAGGGTTGGACATCA
1337376 TAAA
1 TAAA
1337380 CAAAGAAACC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
36 10 0.29
37 25 0.71
ACGTcount: A:0.51, C:0.06, G:0.25, T:0.18
Consensus pattern (37 bp):
TAAAAAAAAGATAAACAGAAGAGAGGGTTGGACATCA
Found at i:1338880 original size:26 final size:27
Alignment explanation
Indices: 1338826--1338880 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1338816 CAAATTCGCA
** *
1338826 ACGCGATTTTAAGATTCGCAATGCAAT
1 ACGCGATTTTAAGATTCAAAACGCAAT
*
1338853 ACGCGA-TTTAAGATTCAAAACGCGAT
1 ACGCGATTTTAAGATTCAAAACGCAAT
1338879 AC
1 AC
1338881 TCCAAAATCG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 18 0.75
27 6 0.25
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.25
Consensus pattern (27 bp):
ACGCGATTTTAAGATTCAAAACGCAAT
Found at i:1338976 original size:21 final size:21
Alignment explanation
Indices: 1338950--1338993 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1338940 GGACGTGTCA
1338950 AATTTCGACTTTCGGGTTGCG
1 AATTTCGACTTTCGGGTTGCG
* *
1338971 AATTTCGATTTTCGTGTTGCG
1 AATTTCGACTTTCGGGTTGCG
1338992 AA
1 AA
1338994 ATTGATTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.25, T:0.41
Consensus pattern (21 bp):
AATTTCGACTTTCGGGTTGCG
Found at i:1339918 original size:32 final size:32
Alignment explanation
Indices: 1339877--1339943 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
1339867 AATTAAATTT
1339877 ATTTTAATTTAATTTAACCTGGTTTGATATCC
1 ATTTTAATTTAATTTAACCTGGTTTGATATCC
1339909 ATTTTAATTTAATTTAACCTGGTTTGATATCC
1 ATTTTAATTTAATTTAACCTGGTTTGATATCC
1339941 ATT
1 ATT
1339944 AATGGAACTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.51
Consensus pattern (32 bp):
ATTTTAATTTAATTTAACCTGGTTTGATATCC
Found at i:1346346 original size:8 final size:8
Alignment explanation
Indices: 1346333--1346359 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
1346323 ATAAAAGTAG
1346333 AATAGTTT
1 AATAGTTT
1346341 AATAGTTT
1 AATAGTTT
1346349 AATAGTTT
1 AATAGTTT
1346357 AAT
1 AAT
1346360 GATTTATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (8 bp):
AATAGTTT
Found at i:1347584 original size:18 final size:18
Alignment explanation
Indices: 1347561--1347595 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1347551 ATGGATTATC
1347561 AGTGGT-CTTTCGGGACAT
1 AGTGGTCCTTT-GGGACAT
1347579 AGTGGTCCTTTGGGACA
1 AGTGGTCCTTTGGGACA
1347596 AATATTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.17, C:0.17, G:0.34, T:0.31
Consensus pattern (18 bp):
AGTGGTCCTTTGGGACAT
Found at i:1348206 original size:21 final size:21
Alignment explanation
Indices: 1348165--1348206 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1348155 TGTAGCAGTA
**
1348165 CTGTAGCAGGGTATCGGTACC
1 CTGTAGCAGGGTATCAATACC
*
1348186 CTGTAGCATGGTATCAATACC
1 CTGTAGCAGGGTATCAATACC
1348207 ATGGCAGTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.26, T:0.26
Consensus pattern (21 bp):
CTGTAGCAGGGTATCAATACC
Found at i:1355256 original size:2 final size:2
Alignment explanation
Indices: 1355249--1355274 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1355239 GAACAAACAC
1355249 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
1355275 GGGTATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1355536 original size:65 final size:68
Alignment explanation
Indices: 1355457--1355615 Score: 171
Period size: 71 Copynumber: 2.3 Consensus size: 68
1355447 AATGAACAAA
* * * * * *
1355457 AACACTTTAAAAAATAAATAAA-TAA-ACG-TGATATTAAAAATTTAAATGAACACGAACCAGAC
1 AACACCTTCAAAAATAAATAAACGAACACGATGATACTAAAAATTTAAATAAACACGAACCAAAC
1355519 ATG
66 ATG
* * * *
1355522 AATACCTTCAAAAATAAATAAACGAACATGAAAATGATACTAAAAATTTAAATAAACATGAATCA
1 AACACCTTCAAAAATAAATAAACGAACACG---ATGATACTAAAAATTTAAATAAACACGAACCA
1355587 AACATG
63 AACATG
*
1355593 AACACCTTCAAAAATAAACAAAC
1 AACACCTTCAAAAATAAATAAAC
1355616 ACAAACATAA
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
65 19 0.25
66 2 0.03
67 2 0.03
71 53 0.70
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (68 bp):
AACACCTTCAAAAATAAATAAACGAACACGATGATACTAAAAATTTAAATAAACACGAACCAAAC
ATG
Found at i:1357084 original size:20 final size:20
Alignment explanation
Indices: 1357059--1357099 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
1357049 AACAATAACC
*
1357059 TGCTACAATGCATCGATGCA
1 TGCTACAATGCACCGATGCA
1357079 TGCTACAATGCACCGATGCA
1 TGCTACAATGCACCGATGCA
1357099 T
1 T
1357100 AAAAACTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (20 bp):
TGCTACAATGCACCGATGCA
Found at i:1357707 original size:22 final size:21
Alignment explanation
Indices: 1357671--1357737 Score: 73
Period size: 21 Copynumber: 3.0 Consensus size: 21
1357661 CACTGAGTGG
1357671 CATATGAAGTTTGTCCCGAAGGA
1 CATAT-AAG-TTGTCCCGAAGGA
*
1357694 CATGTGAA-TATGTCCCGAAGGA
1 CATAT-AAGT-TGTCCCGAAGGA
*
1357716 CCTATAAGTTGTCCCGAAGGA
1 CATATAAGTTGTCCCGAAGGA
1357737 C
1 C
1357738 CTATGAAACC
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
21 16 0.41
22 16 0.41
23 7 0.18
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (21 bp):
CATATAAGTTGTCCCGAAGGA
Found at i:1357730 original size:21 final size:21
Alignment explanation
Indices: 1357681--1357744 Score: 85
Period size: 21 Copynumber: 3.0 Consensus size: 21
1357671 CATATGAAGT
* *
1357681 TTGTCCCGAAGGACATGTGAA
1 TTGTCCCGAAGGACCTATGAA
1357702 TATGTCCCGAAGGACCTAT-AA
1 T-TGTCCCGAAGGACCTATGAA
1357723 GTTGTCCCGAAGGACCTATGAA
1 -TTGTCCCGAAGGACCTATGAA
1357745 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:1359868 original size:23 final size:23
Alignment explanation
Indices: 1359842--1359899 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1359832 CAAAACTTTT
*
1359842 AGTACTCCTTATAAAATATATTC
1 AGTACTCCTTATAAAAGATATTC
*
1359865 AGTACTCCTTATGAAAGATATTC
1 AGTACTCCTTATAAAAGATATTC
1359888 AGTACTCCTTAT
1 AGTACTCCTTAT
1359900 TCAAGTCAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.38
Consensus pattern (23 bp):
AGTACTCCTTATAAAAGATATTC
Found at i:1360019 original size:19 final size:19
Alignment explanation
Indices: 1359995--1360040 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1359985 AGAGAAGCGA
1359995 AAAAGGAAATTCGAGATCG
1 AAAAGGAAATTCGAGATCG
*
1360014 AAAAGGAAATTCGAGATTG
1 AAAAGGAAATTCGAGATCG
1360033 AAAAGGAA
1 AAAAGGAA
1360041 TTTAGGGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.52, C:0.07, G:0.26, T:0.15
Consensus pattern (19 bp):
AAAAGGAAATTCGAGATCG
Found at i:1361801 original size:20 final size:20
Alignment explanation
Indices: 1361776--1361813 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1361766 AACAATAAAG
*
1361776 TAATTGAAATTTGTTTAACA
1 TAATTGAAATTTGGTTAACA
*
1361796 TAATTGAACTTTGGTTAA
1 TAATTGAAATTTGGTTAA
1361814 GGAATGAATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (20 bp):
TAATTGAAATTTGGTTAACA
Found at i:1370394 original size:2 final size:2
Alignment explanation
Indices: 1370387--1370411 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1370377 ATGTCCATTG
1370387 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1370412 TAGTTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1379572 original size:18 final size:18
Alignment explanation
Indices: 1379549--1379586 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1379539 AGGAAGTAAG
1379549 GGAGGCTATTTTCTCTTC
1 GGAGGCTATTTTCTCTTC
1379567 GGAGGCTATTTTCTCTTC
1 GGAGGCTATTTTCTCTTC
1379585 GG
1 GG
1379587 GCAACTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.11, C:0.21, G:0.26, T:0.42
Consensus pattern (18 bp):
GGAGGCTATTTTCTCTTC
Found at i:1401089 original size:19 final size:19
Alignment explanation
Indices: 1401065--1401103 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1401055 TATCATGTTT
1401065 GCATCTTAAATACGAATAA
1 GCATCTTAAATACGAATAA
1401084 GCATCTTAAATACGAATAA
1 GCATCTTAAATACGAATAA
1401103 G
1 G
1401104 GTTTTTTCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (19 bp):
GCATCTTAAATACGAATAA
Found at i:1402313 original size:31 final size:31
Alignment explanation
Indices: 1402275--1402335 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
1402265 ACTCATCCAC
** *
1402275 GTGCCTAACGTTATTAATGTTACCACTTTAG
1 GTGCCTAACGTTACAAATATTACCACTTTAG
*
1402306 GTGCCTAATGTTACAAATATTACCACTTTA
1 GTGCCTAACGTTACAAATATTACCACTTTA
1402336 AGTTTCTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (31 bp):
GTGCCTAACGTTACAAATATTACCACTTTAG
Found at i:1403935 original size:21 final size:21
Alignment explanation
Indices: 1403911--1403965 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
1403901 TCCTTTTATG
1403911 AAAAGGTTAAGTCATTTCATC
1 AAAAGGTTAAGTCATTTCATC
** * * *
1403932 AAAAGGAGAATTCTTTTGATC
1 AAAAGGTTAAGTCATTTCATC
1403953 AAAAGGTTAAGTC
1 AAAAGGTTAAGTC
1403966 CTTTTATCGA
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (21 bp):
AAAAGGTTAAGTCATTTCATC
Found at i:1422575 original size:178 final size:180
Alignment explanation
Indices: 1422170--1422617 Score: 686
Period size: 178 Copynumber: 2.5 Consensus size: 180
1422160 GTTTACTACT
*
1422170 GGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTT-ACATGTTATATTGTTATAGATCGATAC
1 GGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTAAC-TGTTATATTGTTATGGATCGATAC
* * *
1422234 ATTTTGATAAAGTATCGACAGTTTATTGGCACTATAACTTCTTTTCTTTTAAATTCCAAAAGTGT
65 ATTTTTATAAAGTATCGACACTTTATTAGCACTATAACTTC--TTCTTTTAAATTCCAAAAGTGT
* * *
1422299 CGATACTTATAAGGAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTACC
128 CGATACTTATAAGAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACC
* *
1422352 GGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACA
1 GGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTAACTGTTATATTGTTATGGATCGATACA
*
1422417 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTC-TCTTTTAAATTCC-AAAGTGTCGA
66 TTTTTATAAAGTATCGACACTTTATTAGCACTATAACTTCTTCTTTTAAATTCCAAAAGTGTCGA
* *
1422480 TATTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACC
131 TACTTATAAGAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACC
* * ** * *
1422530 TGTTTTATCATTTATAGACAGATTTTGTCATTTTTTTAACTGTTATATTGTTATGGATCGATACA
1 GGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTAACTGTTATATTGTTATGGATCGATACA
1422595 TTTTTATAAAGTATCGACACTTT
66 TTTTTATAAAGTATCGACACTTT
1422618 CAATATATCC
Statistics
Matches: 245, Mismatches: 20, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
178 135 0.55
179 13 0.05
182 96 0.39
183 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (180 bp):
GGTTTTGTCATTTCGAGACCGATTTTGTCATATTTTTAACTGTTATATTGTTATGGATCGATACA
TTTTTATAAAGTATCGACACTTTATTAGCACTATAACTTCTTCTTTTAAATTCCAAAAGTGTCGA
TACTTATAAGAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACC
Found at i:1422727 original size:111 final size:112
Alignment explanation
Indices: 1422488--1423059 Score: 979
Period size: 111 Copynumber: 5.1 Consensus size: 112
1422478 GATATTTATA
* * * * *
1422488 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTATCATTTATAGACAGAT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1422553 TTTGTCATTTTTTTAACTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1422600 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1422665 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1422711 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACATGTTTTGTCATTTAAAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1422776 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
1422822 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTAAAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
1422887 TTTGTCATTTTTTTACCTGTTATATTGTTACGGATCGATACA-TTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
1422933 ATAAAGTATCGACACTTTCAATATATCCGGTAGCACTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
1422998 TTTGTTATTTTTTTACCTGTTATATTGTTATAGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
1423045 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
1423060 AAACCGACAA
Statistics
Matches: 440, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
111 321 0.73
112 119 0.27
ACGTcount: A:0.26, C:0.16, G:0.14, T:0.44
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:1427894 original size:36 final size:36
Alignment explanation
Indices: 1427854--1427923 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
1427844 AACAATATTT
* *
1427854 AAAATTAATTTTTAATGT-TTTAAAATTTTTTCGTCA
1 AAAATAAATATTTAA-GTATTTAAAATTTTTTCGTCA
*
1427890 AAAATAAATATTTAAGTATTTAATATTTTTTCGT
1 AAAATAAATATTTAAGTATTTAAAATTTTTTCGT
1427924 TATAATTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
35 2 0.07
36 28 0.93
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (36 bp):
AAAATAAATATTTAAGTATTTAAAATTTTTTCGTCA
Found at i:1432705 original size:17 final size:17
Alignment explanation
Indices: 1432683--1432721 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1432673 ACAAGAATCT
*
1432683 TCTTCCGCCTTACTGCA
1 TCTTCCGCCTAACTGCA
*
1432700 TCTTCCGCCTAACTGCC
1 TCTTCCGCCTAACTGCA
1432717 TCTTC
1 TCTTC
1432722 TAGCTCGACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.10, C:0.44, G:0.10, T:0.36
Consensus pattern (17 bp):
TCTTCCGCCTAACTGCA
Found at i:1438079 original size:17 final size:18
Alignment explanation
Indices: 1438057--1438094 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1438047 TGTAATGATT
1438057 AAATTTAA-ATA-AATATA
1 AAATTTAATATACAA-ATA
1438074 AAATTTAATATACAAATA
1 AAATTTAATATACAAATA
1438092 AAA
1 AAA
1438095 AATTAAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 9 0.47
19 2 0.11
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATTTAATATACAAATA
Found at i:1438405 original size:16 final size:16
Alignment explanation
Indices: 1438374--1438426 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
1438364 CTATTTAATA
1438374 TAAATCCTAAACAAAT
1 TAAATCCTAAACAAAT
1438390 TAAA-CCTAAACTAAAT
1 TAAATCCTAAAC-AAAT
*
1438406 TAAAT-ATAAACAAAT
1 TAAATCCTAAACAAAT
*
1438421 TTAATC
1 TAAATC
1438427 TAATGCGTGG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 15 0.47
16 17 0.53
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (16 bp):
TAAATCCTAAACAAAT
Found at i:1439646 original size:55 final size:55
Alignment explanation
Indices: 1439526--1439685 Score: 195
Period size: 55 Copynumber: 3.0 Consensus size: 55
1439516 CGAATGACGA
*
1439526 GTCCGCTCCCTATCCGTTTAGGGAGTATAGAACTCGAACAATCTTCAATAAACGG
1 GTCCGCTCCCTATCCGTTTAGGGAGTATAGAACTCGAACAATCTTCAACAAACGG
* * **
1439581 GTCCGTTCCCTATCCGTTTAGGGAGTATAGAACTCGAACAATCTTCAACGAACTT
1 GTCCGCTCCCTATCCGTTTAGGGAGTATAGAACTCGAACAATCTTCAACAAACGG
* * * *
1439636 GTCCACTCCCTATTCC-TTCAGAGAGTATAGGACT----CAATCTTCAACAAACG
1 GTCCGCTCCCTA-TCCGTTTAGGGAGTATAGAACTCGAACAATCTTCAACAAACG
1439686 AGTTTGCTTC
Statistics
Matches: 92, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
51 14 0.15
55 75 0.82
56 3 0.03
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (55 bp):
GTCCGCTCCCTATCCGTTTAGGGAGTATAGAACTCGAACAATCTTCAACAAACGG
Found at i:1439767 original size:37 final size:37
Alignment explanation
Indices: 1439693--1439769 Score: 111
Period size: 37 Copynumber: 2.1 Consensus size: 37
1439683 ACGAGTTTGC
* *
1439693 TTCACTATTCTTCCGTGAAGGCTTATAGATGATTTGT
1 TTCACTACTCTTCCGTGAAGGCTTATAGATGAATTGT
*
1439730 TTCACTACTCTTCCGTGAAGGCTTA-AGTTTGAATTGT
1 TTCACTACTCTTCCGTGAAGGCTTATAG-ATGAATTGT
1439767 TTC
1 TTC
1439770 GAAGGTCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
36 2 0.06
37 34 0.94
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (37 bp):
TTCACTACTCTTCCGTGAAGGCTTATAGATGAATTGT
Done.