Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A03
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: 105315579
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1369460 characters in sequence are not A, C, G, or T
File 322 of 325
Found at i:103734983 original size:22 final size:22
Alignment explanation
Indices: 103734943--103734984 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
103734933 TGATTACCTT
* *
103734943 AAATATTCAGTTTAGTTTCTAA
1 AAATATTCAGTTGAATTTCTAA
*
103734965 AAATATTTAGTTGAATTTCT
1 AAATATTCAGTTGAATTTCT
103734985 GAAATTTCAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.07, G:0.10, T:0.48
Consensus pattern (22 bp):
AAATATTCAGTTGAATTTCTAA
Found at i:103740150 original size:3 final size:3
Alignment explanation
Indices: 103740142--103740172 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
103740132 GATTCTATGC
103740142 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
103740173 GTCGTCTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:103745293 original size:20 final size:20
Alignment explanation
Indices: 103745268--103745315 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
103745258 AAATATAAAT
103745268 ATATATAATAATTATT-TAAC
1 ATATATAAT-ATTATTATAAC
*
103745288 ATATATAATATTTTTATAAC
1 ATATATAATATTATTATAAC
103745308 ATAATATA
1 AT-ATATA
103745316 TTCAACTAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 5 0.20
20 15 0.60
21 5 0.20
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (20 bp):
ATATATAATATTATTATAAC
Found at i:103746081 original size:29 final size:27
Alignment explanation
Indices: 103746049--103746114 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
103746039 AGTCTAATAA
103746049 AAAAATTTAA-AATTTTAAAGGGTTTAATT
1 AAAAATTTAATAATTTTAAA--GTTTAA-T
*
103746078 AAAATTTTTAATAATTTTAAAGTTTAAT
1 AAAA-ATTTAATAATTTTAAAGTTTAAT
103746106 AATAAATTT
1 AA-AAATTT
103746115 TTTTAAATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
28 6 0.19
29 12 0.38
30 5 0.16
31 9 0.28
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (27 bp):
AAAAATTTAATAATTTTAAAGTTTAAT
Found at i:103746113 original size:30 final size:29
Alignment explanation
Indices: 103746043--103746116 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 29
103746033 TTTTTGAGTC
**
103746043 TAATAAAAAAATTTAAAATTTTAAAGGGTT
1 TAATAAAAATTTTTAAAATTTTAAA-GGTT
*
103746073 TAATTAAAATTTTTAATAATTTTAAA-GTT
1 TAATAAAAATTTTTAA-AATTTTAAAGGTT
103746102 TAATAATAAATTTTT
1 TAATAA-AAATTTTT
103746117 TTAAATTGAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 8 0.21
30 21 0.55
31 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (29 bp):
TAATAAAAATTTTTAAAATTTTAAAGGTT
Found at i:103750215 original size:20 final size:21
Alignment explanation
Indices: 103750192--103750242 Score: 68
Period size: 20 Copynumber: 2.4 Consensus size: 21
103750182 ATTTTTTAGA
103750192 TTTTTTTTGAAATTTCGTG-T
1 TTTTTTTTGAAATTTCGTGAT
* *
103750212 TTTTTTTTTAAATTTGGTGAT
1 TTTTTTTTGAAATTTCGTGAT
103750233 TCTTTTTTTG
1 T-TTTTTTTG
103750243 GTGTTTAGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 17 0.65
21 2 0.08
22 7 0.27
ACGTcount: A:0.14, C:0.04, G:0.14, T:0.69
Consensus pattern (21 bp):
TTTTTTTTGAAATTTCGTGAT
Found at i:103750216 original size:21 final size:22
Alignment explanation
Indices: 103750192--103750242 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
103750182 ATTTTTTAGA
103750192 TTTTTTTTGAAATTTCGTG-TT
1 TTTTTTTTGAAATTTCGTGATT
*
103750213 TTTTTTTT-AAATTTGGTGATT
1 TTTTTTTTGAAATTTCGTGATT
*
103750234 CTTTTTTTG
1 TTTTTTTTG
103750243 GTGTTTAGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.14, C:0.04, G:0.14, T:0.69
Consensus pattern (22 bp):
TTTTTTTTGAAATTTCGTGATT
Found at i:103766040 original size:308 final size:308
Alignment explanation
Indices: 103765454--103766604 Score: 1169
Period size: 308 Copynumber: 3.7 Consensus size: 308
103765444 AAGTAGGTCC
* * * * * *** * *
103765454 TGTCTTCCTATATTGGTAG-GAAGTGGATCAAAG-ATGCAGATCTTGTCTTCCCATATTGGTGGC
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
* * * *
103765517 GAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAAGATAACA
65 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATC-AAAGATAGCA
* * *
103765582 GATCCTATCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCTTGTCTTCCTATATTGGT
129 GATCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGATCTTGTCTTCCTATATTGGT
* *
103765647 GGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGGTAG
194 GGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAG
* * *
103765712 CAGATCCTATCTTACTATATTGGTAGGAAGTGGATCGAAGATGCAGATCT
259 CAGATCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCT
*
103765762 TGTCTTCCCATATTGGTGGCGAAGTAGATCGTAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* * * * * *
103765827 AAGTAGATCGAAGGTAGCATATCCTATCTTCCTATATTGGCGTGAAGTAGATCAAAGATAGTAGG
66 AAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCAAAGATAGCAGA
*
103765892 TCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGATCTTGTCTTCCCATATTGGTGG
131 TCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGATCTTGTCTTCCTATATTGGTGG
* * *
103765957 CGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCAAAGATAGTA
196 CGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCA
* *
103766022 GGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGATCT
261 GATCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCT
* *
103766070 TGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTAGCGTG
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
* * * * * * *
103766135 AAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAG-GAAGTGGATCGACGAT-GCAG
66 AAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCAAAGATAGCAG
* * * * * * *
103766198 ATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-CAGAAAGTAGATCTTGTCTTCATGTATTG
130 ATCTTGTCTTCCTATATTGGTAG-GAAGTGGATCGAC-G-ATGCAGATCTTGTCTTCCTATATTG
* * * * * * * * * *
103766262 G-CGTGAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAG-GAAGTGGATCGACGA
192 GTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGG-CGTGAAGTAGATCGAAGA
* * * * *
103766325 T-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCT
256 TAGCAGATCTTGTCTTCCTATATTGGTAG-GAAGTGGATCGAAG-ATGCAGATCT
*** * * * * * * * * * *
103766379 TGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGATAGTAGGTTTTGTCTTCCTATATTGGTAG-
1 TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGT
* * * * * * * *
103766442 GAAGTGGATCGACGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAATAGATCACAGAAAGCA
65 GAAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGG-CGTGAAGTAGATCAAAGATAGCA
* * * * * * * * **
103766506 GATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCAAAGATAACAGGTCCGGTCTTCCTATATTG
129 GATCTTGTCTTCCTATATTGGTAG-GAAGTGGATCGACGAT-GCAGATCTTGTCTTCCTATATTG
* * * * *
103766570 GTAG-GAAGTGGATCGACG-ATGCAGATTTTGTCTTC
192 GTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTC
103766605 CCATACTGGT
Statistics
Matches: 698, Mismatches: 130, Indels: 31
0.81 0.15 0.04
Matches are distributed among these distances:
307 83 0.12
308 466 0.67
309 127 0.18
310 22 0.03
ACGTcount: A:0.27, C:0.16, G:0.26, T:0.31
Consensus pattern (308 bp):
TGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTG
AAGTAGATCGAAGATAGCAGATCTTGTCTTCCTATATTGGCGTGAAGTAGATCAAAGATAGCAGA
TCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGATCTTGTCTTCCTATATTGGTGG
CGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCA
GATCTTGTCTTCCTATATTGGTAGGAAGTGGATCGAAGATGCAGATCT
Found at i:103766630 original size:132 final size:132
Alignment explanation
Indices: 103765473--103766627 Score: 1459
Period size: 132 Copynumber: 8.7 Consensus size: 132
103765463 ATATTGGTAG
* * * * * * * *
103765473 GAAGTGGATCAAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGAAGAAAGCA
1 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAG-GAAGTGGATCGACG-ATGCA
*** * * * * * * *
103765537 GATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAAGATAA-CAGATCCTATCTTCCTATAT
64 GATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCG-CAGA-AAGCAGATCTTGTCTTCATGTAT
*
103765600 TGGTAG-
127 TGG-CGT
* * * * * * * *
103765606 GAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCTATATTGGTGGCGAAGTAGATCGAAGAAAGCA
1 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAG-GAAGTGGATCGACG-ATGCA
*** * * * ** * * *
103765670 GATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAGCAGATCCTATCTT-ACTATATT
64 GATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCA-TGTATT
*
103765733 GGTAG-
128 GG-CGT
* * * * * * * *
103765738 GAAGTGGATCGAAGAT-GCAGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGTA-GAAAGC
1 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAG-GAAGTGGATCG-ACG-ATGC
*** * * * ** * * * * *
103765801 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGGTAGCATATCCTATCTTCCTATATT
63 AGATCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATT
103765865 GGCGT
128 GGCGT
103765870 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
1 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
*
103765935 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATATATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
103766000 GT
131 GT
103766002 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
1 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
*
103766067 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTAGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
103766132 GT
131 GT
103766134 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
1 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
*
103766199 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGTAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
103766264 GT
131 GT
103766266 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
1 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
103766331 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
103766396 GT
131 GT
*
103766398 GAAGTAGATCAAAGATAGTAGGTTTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
1 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
* *
103766463 TCTTGTCTTCCCATATTGGTGGCGAAATAGATCACAGAAAGCAGATCTTGTCTTCATGTATTGGC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
103766528 GT
131 GT
** **
103766530 GAAGTAGATCAAAGATAACAGGTCCGGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
1 GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
* * * *
103766595 TTTTGTCTTCCCATACTGGTAGCGGAGTAGATC
66 TCTTGTCTTCCCATATTGGTGGCGAAGTAGATC
103766628 ACATCCAGTC
Statistics
Matches: 967, Mismatches: 47, Indels: 17
0.94 0.05 0.02
Matches are distributed among these distances:
131 25 0.03
132 821 0.85
133 121 0.13
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (132 bp):
GAAGTAGATCAAAGATAGTAGGTCTTGTCTTCCTATATTGGTAGGAAGTGGATCGACGATGCAGA
TCTTGTCTTCCCATATTGGTGGCGAAGTAGATCGCAGAAAGCAGATCTTGTCTTCATGTATTGGC
GT
Found at i:103771828 original size:25 final size:25
Alignment explanation
Indices: 103771806--103771857 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
103771796 TATCAAATTT
*
103771806 AAGCATAATACAGGGACTAAAATCA
1 AAGCATAATACAGGGAATAAAATCA
103771831 AAGCATAATACAGGGAATAAAATCA
1 AAGCATAATACAGGGAATAAAATCA
103771856 AA
1 AA
103771858 TTTGACCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.15
Consensus pattern (25 bp):
AAGCATAATACAGGGAATAAAATCA
Found at i:103772996 original size:24 final size:24
Alignment explanation
Indices: 103772969--103773017 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
103772959 AACAGTAGAC
103772969 AATTTGTTTATAGAAAATTTAATG
1 AATTTGTTTATAGAAAATTTAATG
103772993 AATTTGTTTATAGAAAATTTAATG
1 AATTTGTTTATAGAAAATTTAATG
103773017 A
1 A
103773018 CCACTTTCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.12, T:0.45
Consensus pattern (24 bp):
AATTTGTTTATAGAAAATTTAATG
Found at i:103779132 original size:19 final size:17
Alignment explanation
Indices: 103779101--103779148 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 17
103779091 TCCAGAAATT
103779101 AAAAAAAGAAAAATTCAG
1 AAAAAAAGAAAAATT-AG
*
103779119 AAAAATAAGTAAAATTAG
1 AAAAA-AAGAAAAATTAG
103779137 -AAAAAAGAAAAA
1 AAAAAAAGAAAAA
103779149 AACACAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 7 0.26
17 4 0.15
18 7 0.26
19 9 0.33
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.12
Consensus pattern (17 bp):
AAAAAAAGAAAAATTAG
Found at i:103781922 original size:22 final size:22
Alignment explanation
Indices: 103781891--103781944 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
103781881 TAGCTTTTTC
* *
103781891 AATTTTAATTTATTAATAAATAA
1 AATTTTAATTCAAT-ATAAATAA
*
103781914 AA-TTTAATTCAATATACATAA
1 AATTTTAATTCAATATAAATAA
103781935 AATTTTAATT
1 AATTTTAATT
103781945 AGGACAAGCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.33
22 16 0.59
23 2 0.07
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
AATTTTAATTCAATATAAATAA
Found at i:103782768 original size:22 final size:22
Alignment explanation
Indices: 103782742--103782795 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
103782732 ATAATAAAAT
*
103782742 AAATAATATATTAAATTAAGGA
1 AAATAATATATTAAATTAAAGA
* * *
103782764 AAATAA-CTCTTAATTTAAAGA
1 AAATAATATATTAAATTAAAGA
103782785 AAATAAATATA
1 AAAT-AATATA
103782796 ATTATCTAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 3
0.73 0.18 0.09
Matches are distributed among these distances:
21 15 0.62
22 8 0.33
23 1 0.04
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (22 bp):
AAATAATATATTAAATTAAAGA
Found at i:103783576 original size:6 final size:6
Alignment explanation
Indices: 103783565--103783595 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
103783555 TGATTTGGTT
103783565 CGGCTC CGGCTC CGGCTC CGGCTC CGGCTC C
1 CGGCTC CGGCTC CGGCTC CGGCTC CGGCTC C
103783596 TCCCCACATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.32, T:0.16
Consensus pattern (6 bp):
CGGCTC
Found at i:103786626 original size:2 final size:2
Alignment explanation
Indices: 103786621--103786645 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
103786611 TCCGCATGTA
103786621 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
103786646 AGGATAGCCC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:103788912 original size:68 final size:69
Alignment explanation
Indices: 103788781--103788912 Score: 230
Period size: 68 Copynumber: 1.9 Consensus size: 69
103788771 TGCACTGATA
*
103788781 ATTTGTTTTCAAAGATTATGAAACATTTACACCCCCAGAGTTCATCAATGAAGAAAAATAGACTC
1 ATTTGTTTTCAAAGATGATGAAACATTTACACCCCCAGAGTTCATCAATGAAGAAAAATAGACTC
103788846 TATT
66 TATT
* *
103788850 ATTTGTTTTCAAAGATGATGAAACATTTACA-TCCCAGAGTTCATCAATGAAGAAACATAGACT
1 ATTTGTTTTCAAAGATGATGAAACATTTACACCCCCAGAGTTCATCAATGAAGAAAAATAGACT
103788913 AAAAACAATC
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
68 30 0.50
69 30 0.50
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (69 bp):
ATTTGTTTTCAAAGATGATGAAACATTTACACCCCCAGAGTTCATCAATGAAGAAAAATAGACTC
TATT
Found at i:103791964 original size:18 final size:18
Alignment explanation
Indices: 103791931--103791965 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
103791921 TCCTCCTCTA
* *
103791931 TCTCCTCTGTATCCTCCG
1 TCTCCTCTGCAGCCTCCG
103791949 TCTCCTCTGCAGCCTCC
1 TCTCCTCTGCAGCCTCC
103791966 ATTTCCAACT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.06, C:0.49, G:0.11, T:0.34
Consensus pattern (18 bp):
TCTCCTCTGCAGCCTCCG
Found at i:103804910 original size:18 final size:20
Alignment explanation
Indices: 103804872--103804909 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
103804862 TTAGTTTTAG
103804872 TTTAAATATATTATTAAAAA
1 TTTAAATATATTATTAAAAA
*
103804892 TTTAAATATCTT-TTAAAA
1 TTTAAATATATTATTAAAA
103804910 TGTTTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATATATTATTAAAAA
Found at i:103805021 original size:22 final size:21
Alignment explanation
Indices: 103805009--103805046 Score: 62
Period size: 19 Copynumber: 1.9 Consensus size: 21
103804999 TTAATTCGAG
103805009 TAAAAAAATTATTAAAATTCA
1 TAAAAAAATTATTAAAATTCA
103805030 TAAAAAAA--ATTAAAATT
1 TAAAAAAATTATTAAAATT
103805047 AAAAATAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 9 0.53
21 8 0.47
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAAAAAATTATTAAAATTCA
Found at i:103810654 original size:257 final size:257
Alignment explanation
Indices: 103810198--103810716 Score: 876
Period size: 257 Copynumber: 2.0 Consensus size: 257
103810188 TTGTCACTTT
* *
103810198 TCAATTTTAAATTGAAGCAAAGAGTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
1 TCAATTTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
*
103810263 GTGTTGAATTTTTCTCAATGACACTAATATGTGAATAACTATTTACTATATTCTTTAGGGATAAC
66 GTGTTGAATCTTTCTCAATGACACTAATATGTGAATAACTATTTACTATATTCTTTAGGGATAAC
* *
103810328 TATTCATATCCAGTTGGATTTGAAGTAATTATTACCACAATAGCGTCTTCAAGTACAGGATATTG
131 TATTCATATCCAGTTGGATTTGAAGTAATTATTACCACAATAACGTCTTCAAGTACAGAATATTG
* * * *
103810393 ATGATGTAGAAAAAGGCAATGTCTTGTTAAACTATTGTCACCTACTATATTTGCTCAACTCA
196 ATGATGTAGAAAAAGACAATGTCTTGTTAAAATATTGTCACCCACTATAATTGCTCAACTCA
* *
103810455 TCAATTTTAAATTGAAACACAGACTGTGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
1 TCAATTTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
* * *
103810520 GTGTTGAATCTTTCTCATTGACACTAATATTTGAATAACTATTTACTATATTCTTTAGGGATAAT
66 GTGTTGAATCTTTCTCAATGACACTAATATGTGAATAACTATTTACTATATTCTTTAGGGATAAC
* * * *
103810585 TATTCATATCCAGTTGGATTTGTAGTAATTATTACTACAATAATGTGTTCAAGTACAGAATATTG
131 TATTCATATCCAGTTGGATTTGAAGTAATTATTACCACAATAACGTCTTCAAGTACAGAATATTG
103810650 ATGATGTAGAAAAAGACAATGTCTTGTTAAAATATTGTCACCCACTATAATTGCTCAACTCA
196 ATGATGTAGAAAAAGACAATGTCTTGTTAAAATATTGTCACCCACTATAATTGCTCAACTCA
103810712 TCAAT
1 TCAAT
103810717 GGTTTGCTAT
Statistics
Matches: 244, Mismatches: 18, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
257 244 1.00
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (257 bp):
TCAATTTTAAATTGAAACAAAGACTATGGGGCATAGTTTTATGACAGTTTGCTTAATTAGATTCA
GTGTTGAATCTTTCTCAATGACACTAATATGTGAATAACTATTTACTATATTCTTTAGGGATAAC
TATTCATATCCAGTTGGATTTGAAGTAATTATTACCACAATAACGTCTTCAAGTACAGAATATTG
ATGATGTAGAAAAAGACAATGTCTTGTTAAAATATTGTCACCCACTATAATTGCTCAACTCA
Found at i:103828825 original size:179 final size:179
Alignment explanation
Indices: 103828525--103828884 Score: 668
Period size: 179 Copynumber: 2.0 Consensus size: 179
103828515 CTAATTCTGC
*
103828525 ATCAAGGTCTGTATTCTTTTAGATTTTTCAATTTGATCCATTTACTTTTAAATTTCACAAATTTA
1 ATCAAGGTCTGTATTCTTTTAGATTTTGCAATTTGATCCATTTACTTTTAAATTTCACAAATTTA
*
103828590 ATCCTTGTGCTTATTTGACTTAAAAATTAAATTCCAATTGAGAAAAATTCTGCCAAGTTTAAATA
66 ATCCTTGTGCTTATTTGACTTAAAAATTAAATCCCAATTGAGAAAAATTCTGCCAAGTTTAAATA
* *
103828655 GGTGTTATCAATTGGATTTTTTCTAATTAGAACTTTAAATATTAATAAT
131 GGTGTTATCAATTGGATTTTTTATAATTAGAACTTTAAATATTAAAAAT
103828704 ATCAAGGTCTGTATTCTTTTAGATTTTGCAATTTGATCCATTTACTTTTAAATTTCACAAATTTA
1 ATCAAGGTCTGTATTCTTTTAGATTTTGCAATTTGATCCATTTACTTTTAAATTTCACAAATTTA
103828769 ATCCTTGTGCTTATTTGACTTAAAAATTAAATCCCAATTGAG-AAAATTGCTGCCAAGTTTAAAT
66 ATCCTTGTGCTTATTTGACTTAAAAATTAAATCCCAATTGAGAAAAATT-CTGCCAAGTTTAAAT
103828833 AGGTGTTATCAATTGGATTTTTTATAATTAGAACTTTAAATATTAAAAAT
130 AGGTGTTATCAATTGGATTTTTTATAATTAGAACTTTAAATATTAAAAAT
103828883 AT
1 AT
103828885 TATAAGTCTA
Statistics
Matches: 176, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
178 6 0.03
179 170 0.97
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (179 bp):
ATCAAGGTCTGTATTCTTTTAGATTTTGCAATTTGATCCATTTACTTTTAAATTTCACAAATTTA
ATCCTTGTGCTTATTTGACTTAAAAATTAAATCCCAATTGAGAAAAATTCTGCCAAGTTTAAATA
GGTGTTATCAATTGGATTTTTTATAATTAGAACTTTAAATATTAAAAAT
Found at i:103844179 original size:18 final size:17
Alignment explanation
Indices: 103844140--103844181 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
103844130 AATTTATTTT
103844140 ATTT-ATTACGTAATTA
1 ATTTAATTACGTAATTA
* *
103844156 AATTAATTATCGTTATTA
1 ATTTAATTA-CGTAATTA
103844174 ATTTAATT
1 ATTTAATT
103844182 GAATCGATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
16 3 0.14
17 4 0.19
18 14 0.67
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (17 bp):
ATTTAATTACGTAATTA
Found at i:103856892 original size:24 final size:23
Alignment explanation
Indices: 103856846--103856892 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
103856836 AATTATAAAT
*
103856846 TTTTTAAAAAATATTATTTTTCA
1 TTTTTAAAAAATATTATTATTCA
* *
103856869 TTTTTATAAATATATTCTTATTCA
1 TTTTTA-AAAAATATTATTATTCA
103856893 ATATCTAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (23 bp):
TTTTTAAAAAATATTATTATTCA
Found at i:103867620 original size:18 final size:18
Alignment explanation
Indices: 103867583--103867617 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
103867573 AGGAAACAAT
*
103867583 TAATAGTATGATTAAAAA
1 TAATAGTATAATTAAAAA
103867601 TAATAGTA-AATTAAAAA
1 TAATAGTATAATTAAAAA
103867618 ATATTATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.31
Consensus pattern (18 bp):
TAATAGTATAATTAAAAA
Found at i:103884148 original size:28 final size:30
Alignment explanation
Indices: 103884116--103884180 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 30
103884106 TAGAGTTGTG
* *
103884116 ATCAAATTAGTCCTT-TATTATT-AAATGA
1 ATCAAATTAGTCATTATATTATTAAAAAGA
* *
103884144 ATCAATTTAGTCATTATATTGTTAAAAAGA
1 ATCAAATTAGTCATTATATTATTAAAAAGA
103884174 ATCAAAT
1 ATCAAAT
103884181 AATGTGAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 13 0.43
29 6 0.20
30 11 0.37
ACGTcount: A:0.43, C:0.09, G:0.08, T:0.40
Consensus pattern (30 bp):
ATCAAATTAGTCATTATATTATTAAAAAGA
Found at i:103892910 original size:32 final size:32
Alignment explanation
Indices: 103892864--103892973 Score: 118
Period size: 31 Copynumber: 3.4 Consensus size: 32
103892854 GATGTCCTTT
*
103892864 AAAATATTTGAAAATTTTAATTAG-GTCCCTTCA
1 AAAAT-TTTAAAAATTTTAATTAGAG-CCCTTCA
* *
103892897 AAAATTTTAAAAATTCTAA-TAGAGCCTTTCA
1 AAAATTTTAAAAATTTTAATTAGAGCCCTTCA
* *
103892928 AAAATTTTAAAAATTTTAATTA-AACCCTCCAA
1 AAAATTTTAAAAATTTTAATTAGAGCCCTTC-A
*
103892960 AAAATTTGAAAAAT
1 AAAATTTTAAAAAT
103892974 CTTATTAATC
Statistics
Matches: 66, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
31 32 0.48
32 29 0.44
33 5 0.08
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (32 bp):
AAAATTTTAAAAATTTTAATTAGAGCCCTTCA
Found at i:103892961 original size:31 final size:31
Alignment explanation
Indices: 103892864--103893016 Score: 105
Period size: 31 Copynumber: 4.9 Consensus size: 31
103892854 GATGTCCTTT
* ** *
103892864 AAAATATTTGAAAATTTTAATTAGGTCCCTTCA
1 AAAAT-TTTAAAAATTTTAATTA-AACCCTCCA
* * * *
103892897 AAAATTTTAAAAATTCTAA-TAGAGCCTTTCA
1 AAAATTTTAAAAATTTTAATTA-AACCCTCCA
103892928 AAAATTTTAAAAATTTTAATTAAACCCTCCAA
1 AAAATTTTAAAAATTTTAATTAAACCCTCC-A
* * * * *
103892960 AAAATTTGAAAAATCTT-ATTAATCTTCTCGA
1 AAAATTTTAAAAATTTTAATTAAAC-CCTCCA
**
103892991 AATCTTTT-AAAATTTTAATTAAACCC
1 AAAATTTTAAAAATTTTAATTAAACCC
103893017 CCTAAGTTTT
Statistics
Matches: 96, Mismatches: 20, Indels: 11
0.76 0.16 0.09
Matches are distributed among these distances:
30 8 0.08
31 50 0.52
32 33 0.34
33 5 0.05
ACGTcount: A:0.44, C:0.14, G:0.05, T:0.38
Consensus pattern (31 bp):
AAAATTTTAAAAATTTTAATTAAACCCTCCA
Found at i:103911086 original size:48 final size:48
Alignment explanation
Indices: 103911030--103911125 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
103911020 GCAGAACAAA
103911030 CCGACCAAGGTCCCACTTGAATATGGACCTTAAAAACCTTCTTCACGG
1 CCGACCAAGGTCCCACTTGAATATGGACCTTAAAAACCTTCTTCACGG
103911078 CCGACCAAGGTCCCACTTGAATATGGACCTTAAAAACCTTCTTCACGG
1 CCGACCAAGGTCCCACTTGAATATGGACCTTAAAAACCTTCTTCACGG
103911126 TAGAAGATTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.29, C:0.31, G:0.17, T:0.23
Consensus pattern (48 bp):
CCGACCAAGGTCCCACTTGAATATGGACCTTAAAAACCTTCTTCACGG
Found at i:103923065 original size:19 final size:19
Alignment explanation
Indices: 103923019--103923066 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
103923009 ATATATATTT
103923019 TAAA-TTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
103923037 TAAATCTTATTTAGGTAGA
1 TAAATTTTATTTAGGTAGA
*
103923056 TAAGTTTTATT
1 TAAATTTTATT
103923067 CATATTCTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (19 bp):
TAAATTTTATTTAGGTAGA
Found at i:103923142 original size:42 final size:42
Alignment explanation
Indices: 103923083--103923171 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 42
103923073 CTAGGAATAT
* * *
103923083 TTTTATTTTATGTTTTAGTAGTTTATTAGGACAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
*
103923125 TTTTCTTTTATATTTTAGTAGTTTATTAGAATAAGGGAACTA
1 TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
103923167 TTTTC
1 TTTTC
103923172 CCAATTAGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.51
Consensus pattern (42 bp):
TTTTCTTTTATATTTTAGTAGTTTATTAGAACAAGGGAACTA
Found at i:103924754 original size:18 final size:18
Alignment explanation
Indices: 103924723--103924757 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
103924713 TCTATTATTA
*
103924723 AGTGGGGAATGTGCAATG
1 AGTGGGGAAGGTGCAATG
*
103924741 AGTGGTGAAGGTGCAAT
1 AGTGGGGAAGGTGCAAT
103924758 TGCTGGGGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.06, G:0.43, T:0.23
Consensus pattern (18 bp):
AGTGGGGAAGGTGCAATG
Found at i:103932426 original size:24 final size:24
Alignment explanation
Indices: 103932399--103932450 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
103932389 TTAGTAAGTC
*
103932399 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
103932423 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
103932447 AAAT
1 AAAT
103932451 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:103934396 original size:24 final size:24
Alignment explanation
Indices: 103934369--103934420 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
103934359 TTAGTAAGTC
103934369 AAATAAACTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
* *
103934393 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
103934417 AAAT
1 AAAT
103934421 CTTCTAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:103939374 original size:14 final size:14
Alignment explanation
Indices: 103939355--103939405 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
103939345 AATAAAATAA
103939355 ATAAATAAGTGAAT
1 ATAAATAAGTGAAT
*** *
103939369 ATAAATAAAACATT
1 ATAAATAAGTGAAT
103939383 AATAAATAAGTGAAT
1 -ATAAATAAGTGAAT
103939398 ATAAATAA
1 ATAAATAA
103939406 AACATTTGAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
14 18 0.64
15 10 0.36
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (14 bp):
ATAAATAAGTGAAT
Found at i:103939386 original size:29 final size:29
Alignment explanation
Indices: 103939354--103939411 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
103939344 AAATAAAATA
103939354 AATAAATAAGTGAATATAAATAAAACATT
1 AATAAATAAGTGAATATAAATAAAACATT
103939383 AATAAATAAGTGAATATAAATAAAACATT
1 AATAAATAAGTGAATATAAATAAAACATT
103939412 TGATTAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (29 bp):
AATAAATAAGTGAATATAAATAAAACATT
Found at i:103952747 original size:19 final size:18
Alignment explanation
Indices: 103952725--103952764 Score: 71
Period size: 19 Copynumber: 2.2 Consensus size: 18
103952715 TGAATAGAAC
103952725 TTATCTACCTAAATAAGAT
1 TTATCTACCTAAATAA-AT
103952744 TTATCTACCTAAATAAAT
1 TTATCTACCTAAATAAAT
103952762 TTA
1 TTA
103952765 AAATATATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (18 bp):
TTATCTACCTAAATAAAT
Found at i:103960282 original size:18 final size:18
Alignment explanation
Indices: 103960259--103960294 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
103960249 AGTAAGAGTA
103960259 AGTTCATTGGCAACACCT
1 AGTTCATTGGCAACACCT
103960277 AGTTCATTGGCAACACCT
1 AGTTCATTGGCAACACCT
103960295 CCCTTCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (18 bp):
AGTTCATTGGCAACACCT
Found at i:103965894 original size:46 final size:45
Alignment explanation
Indices: 103965835--103965991 Score: 233
Period size: 46 Copynumber: 3.4 Consensus size: 45
103965825 ATGAAATGTG
*
103965835 TAAGACCATGGTTGAAAGATACCATGGTAACATGACGAGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGAC-AGAAATGAA
* * *
103965881 TAAGACCATGGTTGAAAGATACCATGGCAGCGTAACATGAAATGAA
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACA-GAAATGAA
*
103965927 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAAATGAG
1 TAAGACCATGGTTGAAAGATACCATGGCAACATGACAG-AAATGAA
*
103965973 TAAGACCATAGTTGAAAGA
1 TAAGACCATGGTTGAAAGA
103965992 CATTATGGCA
Statistics
Matches: 100, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
45 2 0.02
46 98 0.98
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (45 bp):
TAAGACCATGGTTGAAAGATACCATGGCAACATGACAGAAATGAA
Found at i:103966001 original size:92 final size:92
Alignment explanation
Indices: 103965825--103965993 Score: 268
Period size: 92 Copynumber: 1.8 Consensus size: 92
103965815 GCTCTCTGAT
** *
103965825 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGTAACATGACGAGAAATGAATAAGACCAT
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAATAAGACCAT
* *
103965890 GGTTGAAAGATACCATGGCAGCGTAAC
66 AGTTGAAAGACACCATGGCAGCGTAAC
*
103965917 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGAC-AGAAAATGAGTAAGACCA
1 ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGAG-AAATGAATAAGACCA
103965981 TAGTTGAAAGACA
65 TAGTTGAAAGACA
103965994 TTATGGCATC
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
91 2 0.03
92 68 0.97
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.20
Consensus pattern (92 bp):
ATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACATGACGAGAAATGAATAAGACCAT
AGTTGAAAGACACCATGGCAGCGTAAC
Found at i:103966308 original size:16 final size:17
Alignment explanation
Indices: 103966287--103966319 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
103966277 ATGATGGAGC
103966287 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
103966303 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
103966320 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:103968711 original size:42 final size:42
Alignment explanation
Indices: 103968653--103968738 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
103968643 TAGCATGTAC
103968653 ACACACTTAAGGCGCTCTTCAGAATGGCTTGTCTTACAAGTT
1 ACACACTTAAGGCGCTCTTCAGAATGGCTTGTCTTACAAGTT
103968695 ACACACTTAAGGCGCTCTTCAGAATGGCTTGTCTTACAAGTT
1 ACACACTTAAGGCGCTCTTCAGAATGGCTTGTCTTACAAGTT
103968737 AC
1 AC
103968739 TCACCAAAGG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (42 bp):
ACACACTTAAGGCGCTCTTCAGAATGGCTTGTCTTACAAGTT
Found at i:103978889 original size:19 final size:18
Alignment explanation
Indices: 103978854--103978892 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
103978844 CTATAGAGCT
* *
103978854 AATTTTTATATTCTTTTA
1 AATTTTTATAATATTTTA
103978872 AATTTTTATAAATATTTTA
1 AATTTTTAT-AATATTTTA
103978891 AA
1 AA
103978893 AAATTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
AATTTTTATAATATTTTA
Found at i:103981537 original size:16 final size:17
Alignment explanation
Indices: 103981516--103981553 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
103981506 TAGTTGAACC
*
103981516 ATATTTT-ATATTTTTA
1 ATATTTTAATACTTTTA
103981532 ATATTTTAATACTTTTA
1 ATATTTTAATACTTTTA
103981549 A-ATTT
1 ATATTT
103981554 ATAGGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (17 bp):
ATATTTTAATACTTTTA
Found at i:103982491 original size:16 final size:17
Alignment explanation
Indices: 103982462--103982507 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 17
103982452 GCATTTATAT
103982462 AAAATTATAATAAATGAA
1 AAAATTAT-ATAAATGAA
*
103982480 AAAATTAT-TAAAT-TA
1 AAAATTATATAAATGAA
103982495 AAAA-TATATAAAT
1 AAAATTATATAAAT
103982508 TTTTTTAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 3 0.12
15 10 0.38
16 5 0.19
18 8 0.31
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAATTATATAAATGAA
Found at i:103988611 original size:43 final size:43
Alignment explanation
Indices: 103988553--103988636 Score: 168
Period size: 43 Copynumber: 2.0 Consensus size: 43
103988543 CTTTGATCTA
103988553 ATATATAAGAATTAGTTTACCCATTTTTCAATCAAAAGGGAAT
1 ATATATAAGAATTAGTTTACCCATTTTTCAATCAAAAGGGAAT
103988596 ATATATAAGAATTAGTTTACCCATTTTTCAATCAAAAGGGA
1 ATATATAAGAATTAGTTTACCCATTTTTCAATCAAAAGGGA
103988637 CAAAATATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.35
Consensus pattern (43 bp):
ATATATAAGAATTAGTTTACCCATTTTTCAATCAAAAGGGAAT
Found at i:103988645 original size:43 final size:43
Alignment explanation
Indices: 103988555--103988646 Score: 159
Period size: 43 Copynumber: 2.1 Consensus size: 43
103988545 TTGATCTAAT
*
103988555 ATATAAGAATTAGTTTACCCATTTTTCAATCAAAAGGGAATAT
1 ATATAAGAATTAGTTTACCCATTTTTCAATCAAAAGGGAATAA
103988598 ATATAAGAATTAGTTTACCCATTTTTCAATCAAAAGGGACA-AA
1 ATATAAGAATTAGTTTACCCATTTTTCAATCAAAAGGGA-ATAA
103988641 ATATAA
1 ATATAA
103988647 TCTAACTCCT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
43 46 0.98
44 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.33
Consensus pattern (43 bp):
ATATAAGAATTAGTTTACCCATTTTTCAATCAAAAGGGAATAA
Found at i:103990063 original size:19 final size:20
Alignment explanation
Indices: 103990040--103990083 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
103990030 AAAATTACAA
*
103990040 AAAAAATCAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
*
103990060 AAAAATTTAAAATAATTTTT
1 AAAAATTCAAAATAATTTTT
103990080 AAAA
1 AAAA
103990084 CTAAAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTT
Found at i:103990090 original size:19 final size:20
Alignment explanation
Indices: 103990048--103990092 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
103990038 AAAAAAAATC
* *
103990048 AAAATAATTTTTAAAAATTT
1 AAAATAATTTTTAAAAACTA
103990068 AAAATAATTTTT-AAAACTA
1 AAAATAATTTTTAAAAACTA
103990087 AAAATA
1 AAAATA
103990093 GTTATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (20 bp):
AAAATAATTTTTAAAAACTA
Found at i:103993227 original size:13 final size:13
Alignment explanation
Indices: 103993209--103993236 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
103993199 GGATGCTTAT
103993209 CCTTAACCTTAGG
1 CCTTAACCTTAGG
103993222 CCTTAACCTTAGG
1 CCTTAACCTTAGG
103993235 CC
1 CC
103993237 CCAAGCCTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (13 bp):
CCTTAACCTTAGG
Found at i:104002938 original size:19 final size:21
Alignment explanation
Indices: 104002892--104002958 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 21
104002882 TCTTTGAAAT
104002892 TTTTTAAAAATATAAATTTTAGAA
1 TTTTTAAAAAT-T--ATTTTAGAA
*
104002916 TTTTTATAAA-TATTTTA-AA
1 TTTTTAAAAATTATTTTAGAA
*
104002935 -TTTTAAAAATTATTTTATAA
1 TTTTTAAAAATTATTTTAGAA
104002955 TTTT
1 TTTT
104002959 AGAAAGAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
18 8 0.21
19 9 0.24
20 8 0.21
21 3 0.08
22 1 0.03
24 9 0.24
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (21 bp):
TTTTTAAAAATTATTTTAGAA
Found at i:104007772 original size:17 final size:17
Alignment explanation
Indices: 104007750--104007783 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
104007740 ATCCACTAAT
*
104007750 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
104007767 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
104007784 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:104012400 original size:17 final size:17
Alignment explanation
Indices: 104012378--104012411 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
104012368 ATCCACTAAT
*
104012378 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
104012395 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
104012412 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:104014796 original size:19 final size:16
Alignment explanation
Indices: 104014758--104014790 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
104014748 CAAAGATAGT
104014758 TCTTTTTTTACCTTTG
1 TCTTTTTTTACCTTTG
104014774 TCTTTTTTTACCTTTG
1 TCTTTTTTTACCTTTG
104014790 T
1 T
104014791 GGTCTTGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.18, G:0.06, T:0.70
Consensus pattern (16 bp):
TCTTTTTTTACCTTTG
Found at i:104015329 original size:15 final size:15
Alignment explanation
Indices: 104015309--104015346 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
104015299 TTTGCAAATA
104015309 ACAGTTGATGCCGGC
1 ACAGTTGATGCCGGC
104015324 ACAGTTGATGCCGGC
1 ACAGTTGATGCCGGC
104015339 ACAGTTGA
1 ACAGTTGA
104015347 AAAGTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.24, C:0.24, G:0.32, T:0.21
Consensus pattern (15 bp):
ACAGTTGATGCCGGC
Found at i:104038899 original size:26 final size:26
Alignment explanation
Indices: 104038870--104038923 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
104038860 GCCGATCCTT
104038870 AACCATTTAAATGGTGAACAAAATGG
1 AACCATTTAAATGGTGAACAAAATGG
104038896 AACCATTTAAATGGTGAACAAAATGG
1 AACCATTTAAATGGTGAACAAAATGG
104038922 AA
1 AA
104038924 AATACAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.48, C:0.11, G:0.19, T:0.22
Consensus pattern (26 bp):
AACCATTTAAATGGTGAACAAAATGG
Found at i:104049245 original size:17 final size:18
Alignment explanation
Indices: 104049223--104049257 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
104049213 AAAAGGAGTA
*
104049223 ATAATTTTTA-AAATTTT
1 ATAATTTATATAAATTTT
104049240 ATAATTTATATAAATTTT
1 ATAATTTATATAAATTTT
104049258 CCTATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATAATTTATATAAATTTT
Found at i:104051454 original size:23 final size:24
Alignment explanation
Indices: 104051428--104051474 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
104051418 AAAAAAAAAG
*
104051428 GAAATTAAATTATA-AAAATTAAA
1 GAAATCAAATTATATAAAATTAAA
*
104051451 GAAATCAAATTATATCAAATTAAA
1 GAAATCAAATTATATAAAATTAAA
104051475 ATATAGAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.30
Consensus pattern (24 bp):
GAAATCAAATTATATAAAATTAAA
Found at i:104055009 original size:30 final size:29
Alignment explanation
Indices: 104054975--104055031 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
104054965 GTAATTTATG
* * *
104054975 AAAATTGAATCAAATCAAATTTTCATGTTT
1 AAAATCGAATAAAATCAAA-GTTCATGTTT
*
104055005 AAAATCGTATAAAATCAAAGTTCATGT
1 AAAATCGAATAAAATCAAAGTTCATGT
104055032 ATAATTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 7 0.30
30 16 0.70
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.35
Consensus pattern (29 bp):
AAAATCGAATAAAATCAAAGTTCATGTTT
Found at i:104072523 original size:16 final size:16
Alignment explanation
Indices: 104072502--104072534 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
104072492 AAATGTCCCT
104072502 CTATTATTAAATGAAC
1 CTATTATTAAATGAAC
104072518 CTATTATTAAATGAAC
1 CTATTATTAAATGAAC
104072534 C
1 C
104072535 AATTTAGTCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (16 bp):
CTATTATTAAATGAAC
Found at i:104074561 original size:19 final size:19
Alignment explanation
Indices: 104074539--104074575 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
104074529 ATTGTTTGTT
104074539 GTATGTTAT-TTTTAAACAA
1 GTAT-TTATGTTTTAAACAA
104074558 GTATTTATGTTTTAAACA
1 GTATTTATGTTTTAAACA
104074576 TGTGATTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.49
Consensus pattern (19 bp):
GTATTTATGTTTTAAACAA
Found at i:104074732 original size:19 final size:19
Alignment explanation
Indices: 104074693--104074730 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
104074683 AAAGTGAATC
*
104074693 TTGGTCCTTAACTTTCAAA
1 TTGGTCCTTAACTATCAAA
104074712 TTGGTCCTTAAACTATCAA
1 TTGGTCCTT-AACTATCAA
104074731 TTAAGACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (19 bp):
TTGGTCCTTAACTATCAAA
Found at i:104075707 original size:15 final size:15
Alignment explanation
Indices: 104075662--104075708 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
104075652 AATGAGGTTT
*
104075662 TTTTATCTAACTTAA
1 TTTTATCTAATTTAA
104075677 TTATATAT-TAAATTTAA
1 TT-T-TATCT-AATTTAA
104075694 TTTTATCTAATTTAA
1 TTTTATCTAATTTAA
104075709 ACTAGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
15 12 0.44
16 4 0.15
17 11 0.41
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTATCTAATTTAA
Found at i:104089395 original size:103 final size:103
Alignment explanation
Indices: 104089188--104089383 Score: 365
Period size: 103 Copynumber: 1.9 Consensus size: 103
104089178 TCTATACATT
104089188 TTTTAATTTAGAATTTTTATAAATTTTAAATTATTTGTTAACAATATATAATATAAATATTACCA
1 TTTTAATTTAGAATTTTTATAAATTTTAAATTATTTGTTAACAATATATAATATAAATATTACCA
104089253 TGTCAGTATGAAATACACGTAGACTAATATAGAAGTTG
66 TGTCAGTATGAAATACACGTAGACTAATATAGAAGTTG
* *
104089291 TTTTAATTTAGAATTTTTATAAATTTTAAATTATTTGTTAACATTTTATAATATAAATATTACCA
1 TTTTAATTTAGAATTTTTATAAATTTTAAATTATTTGTTAACAATATATAATATAAATATTACCA
*
104089356 TTTCAGTATGAAATACACGTAGACTAAT
66 TGTCAGTATGAAATACACGTAGACTAAT
104089384 GTGGGAGTTG
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 90 1.00
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (103 bp):
TTTTAATTTAGAATTTTTATAAATTTTAAATTATTTGTTAACAATATATAATATAAATATTACCA
TGTCAGTATGAAATACACGTAGACTAATATAGAAGTTG
Found at i:104092407 original size:46 final size:46
Alignment explanation
Indices: 104092355--104092582 Score: 314
Period size: 46 Copynumber: 5.0 Consensus size: 46
104092345 AGTGTGCTCT
*
104092355 CTGATATGAAATGTGTAAGACCATGGTTGAAATATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
104092401 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACAATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
*
104092447 CTGATATGAGATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * **
104092493 GTGACATGAAAAGAATAAGACCATGGTTGAAAGATACCATGGCAAC
1 CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
* * * * * *
104092539 ATGACA-GAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCA
1 CTGATATG-AAATGTGTAAGACCATGGTTGAAAGATACCATGGCA
104092583 TCACGTCAAA
Statistics
Matches: 165, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 1 0.01
46 164 0.99
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.22
Consensus pattern (46 bp):
CTGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAAC
Found at i:104092888 original size:23 final size:25
Alignment explanation
Indices: 104092844--104092889 Score: 60
Period size: 23 Copynumber: 1.9 Consensus size: 25
104092834 ATAAATATAC
*
104092844 ATAAAATATATGGAAATGATGAAGT
1 ATAAAATATATGGAAATAATGAAGT
*
104092869 ATAAAATAT-T-GATATAATGAA
1 ATAAAATATATGGAAATAATGAA
104092890 ATGAATGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 9 0.47
24 1 0.05
25 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.30
Consensus pattern (25 bp):
ATAAAATATATGGAAATAATGAAGT
Found at i:104103526 original size:16 final size:16
Alignment explanation
Indices: 104103505--104103538 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
104103495 ATAAATTATC
104103505 AAAAATAAAATAAATT
1 AAAAATAAAATAAATT
* *
104103521 AAAAATAACATAATTT
1 AAAAATAAAATAAATT
104103537 AA
1 AA
104103539 CCTTTGCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAAATAAATT
Found at i:104108509 original size:18 final size:20
Alignment explanation
Indices: 104108469--104108510 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
104108459 TCTCTTATCA
*
104108469 AAAATTACAAAATAATTTTT
1 AAAATTACAAAATAATTTAT
104108489 AAAATT-CAAAAT-ATTTAT
1 AAAATTACAAAATAATTTAT
104108507 AAAA
1 AAAA
104108511 AATCCCAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATTACAAAATAATTTAT
Found at i:104108511 original size:19 final size:21
Alignment explanation
Indices: 104108463--104108511 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 21
104108453 TTGGTCTCTC
104108463 TTATCAAAAATTACAAAATAAT
1 TTAT-AAAAATTACAAAATAAT
*
104108485 TT-TTAAAATT-CAAAAT-AT
1 TTATAAAAATTACAAAATAAT
104108503 TTATAAAAA
1 TTATAAAAA
104108512 ATCCCAAAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 4 0.17
19 11 0.46
20 6 0.25
21 1 0.04
22 2 0.08
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (21 bp):
TTATAAAAATTACAAAATAAT
Found at i:104111539 original size:98 final size:98
Alignment explanation
Indices: 104111370--104111564 Score: 266
Period size: 98 Copynumber: 2.0 Consensus size: 98
104111360 ACCCTAACGG
* * **
104111370 TTTGTTCGATTAGCTGAAATTTGGTTGCTCGGTTAATTCGAGAATATTGCTATATTCATTGTTTG
1 TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATATTCATTGTTTG
* *
104111435 TTTAAGATTATCATAGAATGAGTAGGAGCATGT
66 TTTAAGATGATCATACAATGAGTAGGAGCATGT
* * *
104111468 TTTGTTCGATGAGCTGAAATTTGTTTGCTTGGTAAATTCGAGAATATCATTATATGT-ATTGTTT
1 TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATAT-TCATTGTTT
* * *
104111532 GTTTAAGATGATGATACATTGTGTAGGAGCATG
65 GTTTAAGATGATCATACAATGAGTAGGAGCATG
104111565 CTTTCTTCAG
Statistics
Matches: 84, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
98 83 0.99
99 1 0.01
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (98 bp):
TTTGTTCGATGAGCTGAAATTTGGTTGCTCGGTAAATTCGAGAATATCACTATATTCATTGTTTG
TTTAAGATGATCATACAATGAGTAGGAGCATGT
Found at i:104111794 original size:186 final size:186
Alignment explanation
Indices: 104111469--104112109 Score: 960
Period size: 186 Copynumber: 3.4 Consensus size: 186
104111459 GGAGCATGTT
* * * * * *
104111469 TTGTTCGATGAGCTGAAATTTGTTTGCTTGGTAAATTCGAGAATATCATTATATGTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
104111534 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
*
104111599 GAACTGTTTATATGCTGCTTCTGAGTCTGCTGAGGCTGCTAATCAACCCCAAAGGC
131 GAACTGTTTATATGCTGCTTCTGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
* ** ** *
104111655 TTGTTCGGTTAGCTGAAATTCAATTGCTCGGTTAATTTGAGAATATCACTATATTTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
* *
104111720 TTAAGACGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTCTAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
* *
104111785 GAGCTGTTTATATGCTGCTTCCGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
131 GAACTGTTTATATGCTGCTTCTGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
* *
104111841 TTGTTCCATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATTTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
* * * *
104111906 CTAAGATGATGATACATAGTGTAGGAGCATACTTTCTTCAGTATGAATCTCATTGGTTTGTATAT
66 TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
* * *
104111971 GAACT-TTCTATATGCTGCTGCTGAGTCTGTTGAGGCTGCTAATCAACCCTAAAGGT
131 GAACTGTT-TATATGCTGCTTCTGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
* ** * **
104112027 TTGTTCAATTAGCTGAAATTTGATTGCTCAATTAATTCAAGAACATTGCTATATGTATTGTTTGT
1 TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
* *
104112092 TTTAGATGATAATACATT
66 TTAAGATGATGATACATT
104112110 TTTTAGTAGT
Statistics
Matches: 411, Mismatches: 43, Indels: 2
0.90 0.09 0.00
Matches are distributed among these distances:
185 2 0.00
186 409 1.00
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.40
Consensus pattern (186 bp):
TTGTTCGATTAGCTGAAATTTGATTGCTCGGTTAATTCAAGAATATCACTATATGTATTGTTTGT
TTAAGATGATGATACATTGTGTAGGAGCATGCTTTCTTCAGTATGAATCTCGTTGGTTTGTATAT
GAACTGTTTATATGCTGCTTCTGAGTCTGTTGAGGCTGCTAATCAACCCCAAAGGC
Found at i:104116675 original size:31 final size:31
Alignment explanation
Indices: 104116629--104116690 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
104116619 AAAACTTGAT
104116629 TTAAATAAAAACTTTCAAATAGTTCAATGAC
1 TTAAATAAAAACTTTCAAATAGTTCAATGAC
* * *
104116660 TTAAATGAAAGCTTTCAAATAGTTCAGTGAC
1 TTAAATAAAAACTTTCAAATAGTTCAATGAC
104116691 CATATTGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.44, C:0.13, G:0.11, T:0.32
Consensus pattern (31 bp):
TTAAATAAAAACTTTCAAATAGTTCAATGAC
Found at i:104119450 original size:18 final size:18
Alignment explanation
Indices: 104119427--104119466 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
104119417 TGTTTCATAT
104119427 AAAA-TTAAATTAATTTAA
1 AAAATTTAAATT-ATTTAA
*
104119445 AAAATTTAAATTTTTTAA
1 AAAATTTAAATTATTTAA
104119463 AAAA
1 AAAA
104119467 ATTATAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATTTAAATTATTTAA
Found at i:104123779 original size:21 final size:21
Alignment explanation
Indices: 104123755--104123796 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
104123745 AAGTGACCAA
104123755 AATGTGAACTTGTTAATAGTT
1 AATGTGAACTTGTTAATAGTT
104123776 AATGTGAACTTGTTAATAGTT
1 AATGTGAACTTGTTAATAGTT
104123797 TAATATTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (21 bp):
AATGTGAACTTGTTAATAGTT
Found at i:104127054 original size:31 final size:31
Alignment explanation
Indices: 104127019--104127089 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
104127009 TCAATATTTG
* *
104127019 ATTTGGTATTTGAGCTTGG-TTTTGATATTCA
1 ATTTGGTACTTGAGCTTGGCTTTAG-TATTCA
* *
104127050 ATTTGTTACTTGAGTTTGGCTTTAGTATTCA
1 ATTTGGTACTTGAGCTTGGCTTTAGTATTCA
*
104127081 ATTTAGTAC
1 ATTTGGTAC
104127090 CTAACATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.21, C:0.08, G:0.20, T:0.51
Consensus pattern (31 bp):
ATTTGGTACTTGAGCTTGGCTTTAGTATTCA
Found at i:104135720 original size:20 final size:22
Alignment explanation
Indices: 104135695--104135734 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
104135685 GTGCTGGTAG
104135695 TTAATTA-T-ATGTATTTTTTT
1 TTAATTATTAATGTATTTTTTT
104135715 TTAATTATTAATGTATTTTT
1 TTAATTATTAATGTATTTTT
104135735 CATGTTCGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (22 bp):
TTAATTATTAATGTATTTTTTT
Found at i:104136427 original size:20 final size:19
Alignment explanation
Indices: 104136390--104136430 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
104136380 TATATATATC
104136390 ATAAAAATGAAAATAAAAT
1 ATAAAAATGAAAATAAAAT
104136409 ATAAAAATCAGAAAA-AAAAT
1 ATAAAAAT--GAAAATAAAAT
104136429 AT
1 AT
104136431 TTCGAAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.40
20 7 0.35
21 5 0.25
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.20
Consensus pattern (19 bp):
ATAAAAATGAAAATAAAAT
Found at i:104140593 original size:67 final size:67
Alignment explanation
Indices: 104140485--104140617 Score: 205
Period size: 67 Copynumber: 2.0 Consensus size: 67
104140475 TGAACAAATT
* *
104140485 ACTCAAAATGATCTAAACTCATGATGATTCAAATTAAAAGACTTAAGCTTAAAACTCGAATGACA
1 ACTCAAAATGATCTAAACCCATAATGATTCAAATTAAAAGACTTAAGCTTAAAACTCGAATGACA
104140550 TG
66 TG
* * *
104140552 ACTCAAAATGATCTAAACCCGTAATGA-TCAAAATTAAAAGACTTAAGTTTCAAACTCGAATGAC
1 ACTCAAAATGATCTAAACCCATAATGATTC-AAATTAAAAGACTTAAGCTTAAAACTCGAATGAC
104140616 AT
65 AT
104140618 AACATAGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
66 2 0.03
67 58 0.97
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.26
Consensus pattern (67 bp):
ACTCAAAATGATCTAAACCCATAATGATTCAAATTAAAAGACTTAAGCTTAAAACTCGAATGACA
TG
Found at i:104152926 original size:9 final size:9
Alignment explanation
Indices: 104152912--104152970 Score: 82
Period size: 9 Copynumber: 6.6 Consensus size: 9
104152902 ATAAGTATAA
*
104152912 AATTAACTG
1 AATTAACCG
*
104152921 AATTAATCG
1 AATTAACCG
104152930 AATTAACCG
1 AATTAACCG
*
104152939 AATTACCCG
1 AATTAACCG
*
104152948 AATTACCCG
1 AATTAACCG
104152957 AATTAACCG
1 AATTAACCG
104152966 AATTA
1 AATTA
104152971 TTTGTATAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 45 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.27
Consensus pattern (9 bp):
AATTAACCG
Found at i:104153005 original size:5 final size:6
Alignment explanation
Indices: 104152990--104153030 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
104152980 AATTATATGT
*
104152990 TTTTTA TTTTTA TTTTTA GTTTTAGA TTTTTA TTTTTA TTT
1 TTTTTA TTTTTA TTTTTA -TTTT-TA TTTTTA TTTTTA TTT
104153031 ATTAAATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 22 0.71
7 8 0.26
8 1 0.03
ACGTcount: A:0.17, C:0.00, G:0.05, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:104158626 original size:17 final size:18
Alignment explanation
Indices: 104158595--104158629 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
104158585 TTGGGAAACG
*
104158595 ATTCAACTCATTTCACTC
1 ATTCAACTCACTTCACTC
104158613 ATTC-ACTCACTTCACTC
1 ATTCAACTCACTTCACTC
104158630 CACCATTACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.26, C:0.37, G:0.00, T:0.37
Consensus pattern (18 bp):
ATTCAACTCACTTCACTC
Found at i:104160518 original size:14 final size:14
Alignment explanation
Indices: 104160499--104160530 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
104160489 TTTATTGTGG
104160499 TTTTAGTCCCTCTA
1 TTTTAGTCCCTCTA
104160513 TTTTAGTCCCTCTA
1 TTTTAGTCCCTCTA
104160527 TTTT
1 TTTT
104160531 TTTAAGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.25, G:0.06, T:0.56
Consensus pattern (14 bp):
TTTTAGTCCCTCTA
Found at i:104162825 original size:29 final size:30
Alignment explanation
Indices: 104162767--104162825 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
104162757 TTATAGGGAC
* *
104162767 TGGATCAAAATTAGCTCTTCTATTATTAAA
1 TGGATCAAAATTAGCTCTTCTACTAGTAAA
104162797 TGGATC-AAATTAG-TCTCTCTACTAGTAAA
1 TGGATCAAAATTAGCTCT-TCTACTAGTAAA
104162826 ACGAATACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 3 0.12
29 17 0.65
30 6 0.23
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (30 bp):
TGGATCAAAATTAGCTCTTCTACTAGTAAA
Found at i:104164893 original size:11 final size:10
Alignment explanation
Indices: 104164852--104164890 Score: 78
Period size: 10 Copynumber: 3.9 Consensus size: 10
104164842 TTAAAGAAGC
104164852 ATTAAAAAAT
1 ATTAAAAAAT
104164862 ATTAAAAAAT
1 ATTAAAAAAT
104164872 ATTAAAAAAT
1 ATTAAAAAAT
104164882 ATTAAAAAA
1 ATTAAAAAA
104164891 ATAATTCAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (10 bp):
ATTAAAAAAT
Found at i:104170766 original size:99 final size:100
Alignment explanation
Indices: 104170628--104171319 Score: 485
Period size: 101 Copynumber: 6.9 Consensus size: 100
104170618 TCTCCCAAAG
* * * * *
104170628 GGGAGACAAGTGGACTATATACAATCTACACGTGACTTTTAAAT-CT-CACGTATTTGTCCTATG
1 GGGAGACAAATGAACTATACACGATCTACACGTGACTTTTAAATGCTACAC--ACTTGTCCTATG
* **
104170691 AGATTTGATGG-TTATAAGTCTTTCATCATAGTTTGA
64 AGATTTGATGGCTTATAAGCCTCCCATCATAGTTTGA
* * * * * **
104170727 GGGAGACAAATGAACTATACACGA-CTTACGCGTGGCTTTTACATGCTCCACACTTGTCCCACAA
1 GGGAGACAAATGAACTATACACGATC-TACACGTGACTTTTAAATGCTACACACTTGTCCTATGA
* * * * **
104170791 GACTTGATGGCTAAATATGCCTCCCATAATAACTTGA
65 GATTTGATGGCT-TATAAGCCTCCCATCATAGTTTGA
* * **
104170828 GGGAGAAAAATGAACTATACACGATCTACACATGACAATTAAATGCTACACACTTGTACC-ATGA
1 GGGAGACAAATGAACTATACACGATCTACACGTGACTTTTAAATGCTACACACTTGT-CCTATGA
* * * *
104170892 GATTTGAGGGCATATAAGCCTCCCATTATA-ATTGA
65 GATTTGATGGCTTATAAGCCTCCCATCATAGTTTGA
* * * ** *
104170927 GGGCAGACAAATGGACTATACACGATCTACACGTGACTTTTAAATCCCAGGCACTTGTCTTATGA
1 GGG-AGACAAATGAACTATACACGATCTACACGTGACTTTTAAATGCTACACACTTGTCCTATGA
* *
104170992 GATTTGATGGC-TAAAAGCCTCCCATCATGGTTTGA
65 GATTTGATGGCTTATAAGCCTCCCATCATAGTTTGA
* * * * * * *
104171027 CGGAGACAAATGAACTATACACGA-CTTGCATGTGGCTTTTACATGCTCCACACTTGT-CTCATA
1 GGGAGACAAATGAACTATACACGATC-TACACGTGACTTTTAAATGCTACACACTTGTCCT-ATG
* **
104171090 AGACTTGAT-GCTATATAAAGCCTCCCATCATAACTTGA
64 AGATTTGATGGCT-TAT-AAGCCTCCCATCATAGTTTGA
* * * * * * * ** * * *
104171128 GAGAAACAAGTGAACTATACACAATCTACACGTGACCTTTACATGTTGTATACATGTCCTACGAG
1 GGGAGACAAATGAACTATACACGATCTACACGTGACTTTTAAATGCTACACACTTGTCCTATGAG
* * * *** * * **
104171193 ATTTGAAGGGCATATAAGGCTTTTATTATAATCAGA
66 ATTTG-ATGGCTTATAAGCCTCCCATCATAGTTTGA
* * * * * * *
104171229 GGGAGACAAGTGGACAATACATGATCTACACGTGATTTTTACATG-TCACACACTTGTCCTACGA
1 GGGAGACAAATGAACTATACACGATCTACACGTGACTTTTAAATGCT-ACACACTTGTCCTATGA
*
104171293 GATTTGATGGC-TAT-A-TCTCCCATCATA
65 GATTTGATGGCTTATAAGCCTCCCATCATA
104171320 ATCTCTCCCA
Statistics
Matches: 458, Mismatches: 115, Indels: 42
0.74 0.19 0.07
Matches are distributed among these distances:
97 7 0.02
98 6 0.01
99 131 0.29
100 90 0.20
101 212 0.46
102 10 0.02
103 2 0.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (100 bp):
GGGAGACAAATGAACTATACACGATCTACACGTGACTTTTAAATGCTACACACTTGTCCTATGAG
ATTTGATGGCTTATAAGCCTCCCATCATAGTTTGA
Found at i:104171196 original size:300 final size:300
Alignment explanation
Indices: 104170628--104171305 Score: 853
Period size: 300 Copynumber: 2.3 Consensus size: 300
104170618 TCTCCCAAAG
* * * *
104170628 GGGAGACAAGTGGACTATATACAATCTACACGTGACTTTTAAATCTCACGTATTTGTCCTATGAG
1 GGGAGACAAGTGGACTATACACGATCTACACGTGACTTTTAAATCTCACGCACTTGTCCTATGAG
* * * ** * *
104170693 ATTTGATGGTTATAAGTCTTTCATCATAGTTTGAGGGAGACAAATGAACTATACACGACTTACGC
66 ATTTGATGGCTAAAAGCCTCCCATCATAGTTTGACGGAGACAAATGAACTATACACGACTTACAC
*
104170758 GTGGCTTTTACATGCTCCACACTTGTCCCACAAGACTTGATGGCTAAATATGCCTCCCATAATAA
131 GTGGCTTTTACATGCTCCACACTTGTCCCACAAGACTTGATGGCTAAATAAGCCTCCCATAATAA
* *
104170823 CTTGAGGGAGAAAAATGAACTATACACGATCTACACATGACAATTAAATGCTACACACTTGTACC
196 CTTGA-GGAGAAAAATGAACTATACACAATCTACACATGACAATTAAATGCTACACACATGTACC
* *
104170888 ATGAGATTTG-AGGGCATATAAGCCTCCCATTATAAT-TGA
260 ACGAGATTTGAAGGGCATATAAGCCTCCCATTATAATCAGA
* * * *
104170927 GGGCAGACAAATGGACTATACACGATCTACACGTGACTTTTAAATCCCAGGCACTTGTCTTATGA
1 GGG-AGACAAGTGGACTATACACGATCTACACGTGACTTTTAAATCTCACGCACTTGTCCTATGA
* *
104170992 GATTTGATGGCTAAAAGCCTCCCATCATGGTTTGACGGAGACAAATGAACTATACACGACTTGCA
65 GATTTGATGGCTAAAAGCCTCCCATCATAGTTTGACGGAGACAAATGAACTATACACGACTTACA
* * * * *
104171057 TGTGGCTTTTACATGCTCCACACTTGTCTCATAAGACTTGAT-GCTATATAAAGCCTCCCATCAT
130 CGTGGCTTTTACATGCTCCACACTTGTCCCACAAGACTTGATGGCTAAAT-AAGCCTCCCATAAT
* ** * * ** *
104171121 AACTTGA-GAGAAACAAGTGAACTATACACAATCTACACGTGACCTTTACATGTTGTATACATGT
194 AACTTGAGGAGAAA-AA-TGAACTATACACAATCTACACATGACAATTAAATGCTACACACATGT
* ***
104171185 -CCTACGAGATTTGAAGGGCATATAAGGCTTTTATTATAATCAGA
257 ACC-ACGAGATTTGAAGGGCATATAAGCCTCCCATTATAATCAGA
* * * * * * *
104171229 GGGAGACAAGTGGACAATACATGATCTACACGTGATTTTTACATGTCACACACTTGTCCTACGAG
1 GGGAGACAAGTGGACTATACACGATCTACACGTGACTTTTAAATCTCACGCACTTGTCCTATGAG
104171294 ATTTGATGGCTA
66 ATTTGATGGCTA
104171306 TATCTCCCAT
Statistics
Matches: 322, Mismatches: 50, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
298 6 0.02
299 13 0.04
300 213 0.66
301 85 0.26
302 5 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (300 bp):
GGGAGACAAGTGGACTATACACGATCTACACGTGACTTTTAAATCTCACGCACTTGTCCTATGAG
ATTTGATGGCTAAAAGCCTCCCATCATAGTTTGACGGAGACAAATGAACTATACACGACTTACAC
GTGGCTTTTACATGCTCCACACTTGTCCCACAAGACTTGATGGCTAAATAAGCCTCCCATAATAA
CTTGAGGAGAAAAATGAACTATACACAATCTACACATGACAATTAAATGCTACACACATGTACCA
CGAGATTTGAAGGGCATATAAGCCTCCCATTATAATCAGA
Found at i:104171328 original size:15 final size:15
Alignment explanation
Indices: 104171308--104171338 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
104171298 GATGGCTATA
104171308 TCTCCCATCATAATC
1 TCTCCCATCATAATC
104171323 TCTCCCATCATAATC
1 TCTCCCATCATAATC
104171338 T
1 T
104171339 GAGATAGACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.39, G:0.00, T:0.35
Consensus pattern (15 bp):
TCTCCCATCATAATC
Found at i:104172334 original size:21 final size:22
Alignment explanation
Indices: 104172291--104172335 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
104172281 AACCATTAGT
*
104172291 ATTAATGTGTCGAGTAACGAAA
1 ATTAATGTGACGAGTAACGAAA
* *
104172313 ATTAATG-GACGAGTGACTAAA
1 ATTAATGTGACGAGTAACGAAA
104172334 AT
1 AT
104172336 ATAACAACTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.42, C:0.09, G:0.22, T:0.27
Consensus pattern (22 bp):
ATTAATGTGACGAGTAACGAAA
Found at i:104176063 original size:30 final size:30
Alignment explanation
Indices: 104176029--104176112 Score: 102
Period size: 29 Copynumber: 2.8 Consensus size: 30
104176019 TAAGGGGTTC
104176029 AATTTTTTTTATCAACTTTTAATGGGCC-CA
1 AATTTTTTTTATCAACTTTTAA-GGGCCTCA
* *
104176059 AATTTATTTTT-TTAGCTTTTAAGGGCCTCA
1 AATTT-TTTTTATCAACTTTTAAGGGCCTCA
*
104176089 AA-TTTTTTTACCAACTTTTAAGGG
1 AATTTTTTTTATCAACTTTTAAGGG
104176113 ACTTAAAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
28 5 0.11
29 18 0.39
30 18 0.39
31 5 0.11
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (30 bp):
AATTTTTTTTATCAACTTTTAAGGGCCTCA
Found at i:104176097 original size:29 final size:30
Alignment explanation
Indices: 104176029--104176109 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 30
104176019 TAAGGGGTTC
104176029 AATTTTTTTTATCAACTTTTAATGGGCCCA
1 AATTTTTTTTATCAACTTTTAATGGGCCCA
* *
104176059 AATTTATTTTT-TTAGCTTTTAA-GGGCCTCA
1 AATTT-TTTTTATCAACTTTTAATGGGCC-CA
*
104176089 AA-TTTTTTTACCAACTTTTAA
1 AATTTTTTTTATCAACTTTTAA
104176110 GGGACTTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
28 5 0.12
29 15 0.35
30 18 0.42
31 5 0.12
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (30 bp):
AATTTTTTTTATCAACTTTTAATGGGCCCA
Found at i:104185613 original size:28 final size:28
Alignment explanation
Indices: 104185581--104185640 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 28
104185571 TTTCTAAAAC
104185581 TTTAGAAAATATATA-ATTTTTTTTAATT
1 TTTAGAAAATATATAGA-TTTTTTTAATT
**
104185609 TTTAGAATTTATATAGATTTTTTTAATT
1 TTTAGAAAATATATAGATTTTTTTAATT
104185637 TTTA
1 TTTA
104185641 AGTGATAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 28 0.97
29 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (28 bp):
TTTAGAAAATATATAGATTTTTTTAATT
Found at i:104187431 original size:18 final size:17
Alignment explanation
Indices: 104187405--104187440 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
104187395 TTTACTACCT
104187405 TTAAATAATAAATAAAAA
1 TTAAATAAT-AATAAAAA
*
104187423 TTAATTAATAATAAAAA
1 TTAAATAATAATAAAAA
104187440 T
1 T
104187441 ATATAGTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAATAATAATAAAAA
Found at i:104188439 original size:16 final size:16
Alignment explanation
Indices: 104188420--104188463 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
104188410 TTTTGTTGAG
*
104188420 TCATTTTAGGTTT-AGA
1 TCATTTTGGGTTTCA-A
*
104188436 TCATTTCGGGTTTCAA
1 TCATTTTGGGTTTCAA
104188452 TCATTTTGGGTT
1 TCATTTTGGGTT
104188464 ATTTGTTTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 23 0.96
17 1 0.04
ACGTcount: A:0.18, C:0.11, G:0.20, T:0.50
Consensus pattern (16 bp):
TCATTTTGGGTTTCAA
Found at i:104192144 original size:16 final size:16
Alignment explanation
Indices: 104192083--104192135 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
104192073 CTAGATTCAG
* **
104192083 AAAATGATCCAAATAA
1 AAAATAATCCAAATTC
* * *
104192099 AAAATTATCTAAATTT
1 AAAATAATCCAAATTC
104192115 AAAATAATCCAAATTC
1 AAAATAATCCAAATTC
104192131 AAAAT
1 AAAAT
104192136 GATTCAAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.28
Consensus pattern (16 bp):
AAAATAATCCAAATTC
Found at i:104195250 original size:11 final size:10
Alignment explanation
Indices: 104195235--104195328 Score: 55
Period size: 10 Copynumber: 8.6 Consensus size: 10
104195225 AAAAAAAAAA
104195235 TTAAAAAA-T
1 TTAAAAAATT
104195244 TTATAAAAATT
1 TTA-AAAAATT
*
104195255 TTAAAATTTATGTT
1 TTAAAA---A-ATT
104195269 TTAAAAAATAT
1 TTAAAAAAT-T
*
104195280 ATAAAAAATT
1 TTAAAAAATT
*
104195290 CTAAAAAATTCT
1 TTAAAAAA-T-T
*
104195302 TTAAAATATT
1 TTAAAAAATT
*
104195312 TTAAAAATTT
1 TTAAAAAATT
104195322 TCTAAAA
1 T-TAAAA
104195329 TAATAATTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 18
0.72 0.09 0.19
Matches are distributed among these distances:
9 3 0.04
10 27 0.40
11 21 0.31
12 7 0.10
13 1 0.01
14 8 0.12
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.41
Consensus pattern (10 bp):
TTAAAAAATT
Found at i:104195253 original size:18 final size:18
Alignment explanation
Indices: 104195230--104195265 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
104195220 TCAACAAAAA
104195230 AAAAATTAAAAAATTTAT
1 AAAAATTAAAAAATTTAT
**
104195248 AAAAATTTTAAAATTTAT
1 AAAAATTAAAAAATTTAT
104195266 GTTTTAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
AAAAATTAAAAAATTTAT
Found at i:104195432 original size:16 final size:16
Alignment explanation
Indices: 104195413--104195443 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
104195403 TTGAATTTTT
104195413 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
104195429 TTTCAAATTTATATG
1 TTTCAAATATATATG
104195444 CTTTAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:104203865 original size:26 final size:26
Alignment explanation
Indices: 104203836--104203891 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
104203826 ATAATTAATT
* *
104203836 AATTATAATTTA-ATATAATTGATAAA
1 AATTAT-ATTTATATAAAATTAATAAA
*
104203862 AATTATTTTTATATAAAATTAATAAA
1 AATTATATTTATATAAAATTAATAAA
104203888 AATT
1 AATT
104203892 CGTAAATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (26 bp):
AATTATATTTATATAAAATTAATAAA
Found at i:104205328 original size:21 final size:21
Alignment explanation
Indices: 104205262--104205329 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
104205252 GAATTCAATG
*
104205262 TTCAATTTGGTATCTAGATTTGGT
1 TTCAATTTGGTA-CTAGAATT--T
*
104205286 TTCAATGTTGGTAC-CGAATTT
1 TTCAAT-TTGGTACTAGAATTT
* *
104205307 TTCAATTTGGTACTTGAGTTT
1 TTCAATTTGGTACTAGAATTT
104205328 TT
1 TT
104205330 TTTTCTTGGT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
20 7 0.18
21 14 0.37
23 4 0.11
24 7 0.18
25 6 0.16
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.50
Consensus pattern (21 bp):
TTCAATTTGGTACTAGAATTT
Found at i:104206225 original size:6 final size:6
Alignment explanation
Indices: 104206214--104206238 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
104206204 TTTCATCTGA
104206214 TTAATT TTAATT TTAATT TTAATT T
1 TTAATT TTAATT TTAATT TTAATT T
104206239 ATTCATTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:104210509 original size:15 final size:15
Alignment explanation
Indices: 104210489--104210522 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
104210479 AATTGATACT
104210489 TAAACTTGAAAATCG
1 TAAACTTGAAAATCG
104210504 TAAACTTGAAAATCG
1 TAAACTTGAAAATCG
104210519 TAAA
1 TAAA
104210523 TTAATTTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (15 bp):
TAAACTTGAAAATCG
Found at i:104216643 original size:33 final size:33
Alignment explanation
Indices: 104216604--104216672 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
104216594 ATATAAAATG
* * *
104216604 ACAACAAAACAATTGAAAAACGATAAGAAAACA
1 ACAACAAAACAATAGAAAAACAACAAGAAAACA
*
104216637 ACAACAAAACAATAGAAAAACAACAATAAAACA
1 ACAACAAAACAATAGAAAAACAACAAGAAAACA
104216670 ACA
1 ACA
104216673 GTTTTTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.70, C:0.17, G:0.06, T:0.07
Consensus pattern (33 bp):
ACAACAAAACAATAGAAAAACAACAAGAAAACA
Found at i:104219684 original size:197 final size:194
Alignment explanation
Indices: 104219186--104219850 Score: 913
Period size: 197 Copynumber: 3.4 Consensus size: 194
104219176 ATTCTTTATA
* * * * *
104219186 TAATTCTGGTCAGTAACATCATCAATTATTAGTTTTTTAGAATGACCAATAGAGGCATGAAGTTT
1 TAATTCTGGTCAATAACAACATCAATTATTAG-TGTTTAGAATGATCAATAGAGGAATGAAGTTT
* * * *
104219251 TTTGCGT-GGTCTGTGCTTTGTTGTACCTTCTCAGGGCTGCTATAAGTAGTTTTGTTCTTGTGTG
65 TTTGC-TCGGTTTATGCTTTGTT-TACCTTGTCAGGGCTGCTATAAGGAGTTTTGTTCTTGTGTG
*
104219315 TTTATGTTGAAGTTATTTGTTGT-ACTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGT
128 TTTATGTTGAAGTTATTTGCTGTAACTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGT
104219379 GG
193 GG
* * * *
104219381 TAGTTCTGGTCCATAACAGCATCAATTATTAGTGATTA-AATGATCAATAGAGGAATGAAGTTTT
1 TAATTCTGGTCAATAACAACATCAATTATTAGTGTTTAGAATGATCAATAGAGGAATGAAGTTTT
* *
104219445 TTGCTCGGTTTGTGCTTTGTTTTACCTTGTCAGGGCTGCTATAAGGAGTTCTGTTCTTGTGTGTT
66 TTGCTCGGTTTATGCTTTG-TTTACCTTGTCAGGGCTGCTATAAGGAGTTTTGTTCTTGTGTGTT
* *
104219510 TATGTTGAAGTTATATGCTGTAATTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGTGG
130 TATGTTGAAGTTATTTGCTGTAACTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGTGG
* * *
104219575 TAATCCCGGTCAATAACAACATCAATTATTAGAGTTTAGAATATGATCAATAGAGGAATGAAGTT
1 TAATTCTGGTCAATAACAACATCAATTATTAGTGTTTAG-A-ATGATCAATAGAGGAATGAAGTT
*
104219640 TTTTGCTCGGTTTATGCTTCGTTTCACCTTGTCAGGGCTGCTATAAGGAGTTTTGTTCTTGTGTG
64 TTTTGCTCGGTTTATGCTTTGTTT-ACCTTGTCAGGGCTGCTATAAGGAGTTTTGTTCTTGTGTG
* * * * * * * *
104219705 TTTATGTTGAAGTTATTTGCTGTAACTATACAGTTCGTTTGTCGGTCTAAGCATATCAACAATAT
128 TTTATGTTGAAGTTATTTGCTGTAACTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGT
104219770 GG
193 GG
** * * *
104219772 TAATTCTGGTCAATAATGACATCAATTATTACTGTTTCGAATGATCAGTAGAGGAATGAAGTTTT
1 TAATTCTGGTCAATAACAACATCAATTATTAGTGTTTAGAATGATCAATAGAGGAATGAAGTTTT
* *
104219837 TTTCTTGGTTTATG
66 TTGCTCGGTTTATG
104219851 TATGTTTTAA
Statistics
Matches: 418, Mismatches: 45, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
192 1 0.00
193 99 0.24
194 79 0.19
195 64 0.15
196 5 0.01
197 170 0.41
ACGTcount: A:0.25, C:0.12, G:0.21, T:0.42
Consensus pattern (194 bp):
TAATTCTGGTCAATAACAACATCAATTATTAGTGTTTAGAATGATCAATAGAGGAATGAAGTTTT
TTGCTCGGTTTATGCTTTGTTTACCTTGTCAGGGCTGCTATAAGGAGTTTTGTTCTTGTGTGTTT
ATGTTGAAGTTATTTGCTGTAACTATATAGTTCATTTATTGTTTTAAGCATATCAACCATGTGG
Found at i:104220407 original size:13 final size:14
Alignment explanation
Indices: 104220385--104220413 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
104220375 ATTACGGCTC
104220385 TTTTTCTTTTTTTG
1 TTTTTCTTTTTTTG
104220399 TTTTT-TTTTTTTG
1 TTTTTCTTTTTTTG
104220412 TT
1 TT
104220414 GAATGGTCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (14 bp):
TTTTTCTTTTTTTG
Found at i:104234344 original size:31 final size:31
Alignment explanation
Indices: 104234301--104234359 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
104234291 TTTGGTCTGG
* *
104234301 GTACTAAATTGAACATTAAAGCTAAATTTAA
1 GTACCAAATTGAACATTAAAGATAAATTTAA
*
104234332 GTACCAAATTGAACATTGAAGATAAATT
1 GTACCAAATTGAACATTAAAGATAAATT
104234360 CAAATATCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.10, G:0.12, T:0.31
Consensus pattern (31 bp):
GTACCAAATTGAACATTAAAGATAAATTTAA
Found at i:104238622 original size:16 final size:16
Alignment explanation
Indices: 104238601--104238636 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
104238591 TCAATATTCA
104238601 AAATTAACCTCAATCT
1 AAATTAACCTCAATCT
* *
104238617 AAATTAACTTTAATCT
1 AAATTAACCTCAATCT
104238633 AAAT
1 AAAT
104238637 AAGTCAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (16 bp):
AAATTAACCTCAATCT
Found at i:104241338 original size:19 final size:19
Alignment explanation
Indices: 104241316--104241354 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
104241306 TATATTATAA
* *
104241316 ATTACATAATATATAAAAT
1 ATTACAAAATATAAAAAAT
*
104241335 ATTACAAAATTTAAAAAAT
1 ATTACAAAATATAAAAAAT
104241354 A
1 A
104241355 ACGTGCAAGG
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:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTACAAAATATAAAAAAT
Found at i:104251182 original size:60 final size:59
Alignment explanation
Indices: 104251071--104251187 Score: 144
Period size: 60 Copynumber: 2.0 Consensus size: 59
104251061 ACATAAGTAA
* * **
104251071 TTAATTAGAACAAAAAAAACTTAATTACCAAATTGAACATTGAAGTTAAACTCAGGTGC
1 TTAATTAGAACAAAAAAAACTCAAGTACCAAATTGAACATTGAAGCCAAACTCAGGTGC
* * * * *
104251130 TTAATTGGGACAATAAAAAACTCAAGTACCAACTTGAATATTGAAGCCAAACTTAGGT
1 TTAATTAGAACAA-AAAAAACTCAAGTACCAAATTGAACATTGAAGCCAAACTCAGGT
104251188 ACCAATTTGA
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
59 11 0.23
60 37 0.77
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (59 bp):
TTAATTAGAACAAAAAAAACTCAAGTACCAAATTGAACATTGAAGCCAAACTCAGGTGC
Found at i:104251190 original size:31 final size:30
Alignment explanation
Indices: 104251155--104251261 Score: 117
Period size: 31 Copynumber: 3.5 Consensus size: 30
104251145 AAAAACTCAA
104251155 GTACCAACTTGAATATTGAAGCCAAACTTAG
1 GTACCAA-TTGAATATTGAAGCCAAACTTAG
* * *
104251186 GTACCAATTTGACTATTGAAGCCAAACTCAA
1 GTACCAA-TTGAATATTGAAGCCAAACTTAG
* * *
104251217 GTACCAAATTGAACATTAAAACCAAACTTAG
1 GTACC-AATTGAATATTGAAGCCAAACTTAG
*
104251248 ATACCAATT-AATAT
1 GTACCAATTGAATAT
104251262 ATTAACCCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
29 4 0.06
30 4 0.06
31 53 0.84
32 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (30 bp):
GTACCAATTGAATATTGAAGCCAAACTTAG
Found at i:104253021 original size:18 final size:19
Alignment explanation
Indices: 104252998--104253043 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
104252988 TGAATCGGTT
104252998 AAATTATTAGT-ATTGTTA
1 AAATTATTAGTAATTGTTA
*
104253016 AAATTAAT-GTAATTGTTA
1 AAATTATTAGTAATTGTTA
* *
104253034 GAATAATTAG
1 AAATTATTAG
104253044 ATAGGAACAC
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 2 0.09
18 19 0.86
19 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.13, T:0.43
Consensus pattern (19 bp):
AAATTATTAGTAATTGTTA
Found at i:104255998 original size:350 final size:351
Alignment explanation
Indices: 104255363--104256040 Score: 1019
Period size: 350 Copynumber: 1.9 Consensus size: 351
104255353 AAGACGGATT
* * * *
104255363 ACTAAGCTTTAGCCCTTACCTCGAAGTAATTTAAGGTTATACTCTATAGTTTTTGGATGATGACA
1 ACTAAGCTGTAGCCCTTACCTCGAAGTAATTTAAGGCTATACTATATAGTTCTTGGATGATGACA
*
104255428 ATCTATGGAAGTAATTGCGAGTAACTTCTCATGATATATTTCTATATATAATGTTTGCTGGTTGA
66 ATCTATGGAAGTAATTGCGAGTAAATTCTCATGATATATTTCTATATATAATGTTTGCTGGTTGA
* * * * *
104255493 TCATGAGACTTCGATAGGGACTTAAGGGGTTAGTTTTGCTTATATAGAAACTCTGGTAAATGTTG
131 TCATGAGACTTCGATAGGGACTTAAGGAGTTAGCTTTGCTTACAAAGAAACTCTGGAAAATGTTG
* * *
104255558 ATGGTTGTTTCTGCTGAAATCATACCTATTTCAGCCATTTTATTTGTTGATTTCCTAGCTTGTGA
196 ATGGTTGTTTCTGCTAAAATCAAACATATTTCAGCCATTTTATTTGTTGATTTCCTAGCTTGTGA
* * * * *
104255623 TTTTTTTGCTCCGTTGTAGATTTTCCTATGCAGAATTCTGCTAGGTGGTTGAGTTTCCTTGTAGA
261 TTTTTTTGCTCCGTTGTAGATTTTCCTACGCAGAATTATGCTAGGTGGTCGAGATTCATTGTAGA
104255688 ACTTTAGCCACTACCAATAATGAATC
326 ACTTTAGCCACTACCAATAATGAATC
*
104255714 ACTAAGCTGTAGCCCTTACCTTGAAGTAATTTAAGGCTATACTATATAG-TCTTGGATGATGACA
1 ACTAAGCTGTAGCCCTTACCTCGAAGTAATTTAAGGCTATACTATATAGTTCTTGGATGATGACA
* *
104255778 ATCTATGGAAGTAATTGTGAGTAAATTCTCATGATGTATTTCTATATATAATGTTTGCTGGTTGA
66 ATCTATGGAAGTAATTGCGAGTAAATTCTCATGATATATTTCTATATATAATGTTTGCTGGTTGA
104255843 TCATGAGACTTCGATA-GGACTT-AGGAAG-TAGACTTT-CTTACAAAGAAACTCTGCGAAAAT-
131 TCATGAGACTTCGATAGGGACTTAAGG-AGTTAG-CTTTGCTTACAAAGAAACTCTG-GAAAATG
* *
104255903 TTGATGGTTGTTTCTGCTAAAATCAAACATATTTCCGCCATTTTATTTGTTGATTTCGTAGCTTG
193 TTGATGGTTGTTTCTGCTAAAATCAAACATATTTCAGCCATTTTATTTGTTGATTTCCTAGCTTG
* * *
104255968 TGA-TTTTTTGCTCTGTTGTCGATTATTTTCCTACGCAGAATTATGTTAGGTGGTCGAGATTCAT
258 TGATTTTTTTGCTCCGTTGT--A-GATTTTCCTACGCAGAATTATGCTAGGTGGTCGAGATTCAT
104256032 TGTAGAACT
320 TGTAGAACT
104256041 ATAGGTTTGA
Statistics
Matches: 295, Mismatches: 26, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
347 15 0.05
348 84 0.28
349 16 0.05
350 135 0.46
351 45 0.15
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.40
Consensus pattern (351 bp):
ACTAAGCTGTAGCCCTTACCTCGAAGTAATTTAAGGCTATACTATATAGTTCTTGGATGATGACA
ATCTATGGAAGTAATTGCGAGTAAATTCTCATGATATATTTCTATATATAATGTTTGCTGGTTGA
TCATGAGACTTCGATAGGGACTTAAGGAGTTAGCTTTGCTTACAAAGAAACTCTGGAAAATGTTG
ATGGTTGTTTCTGCTAAAATCAAACATATTTCAGCCATTTTATTTGTTGATTTCCTAGCTTGTGA
TTTTTTTGCTCCGTTGTAGATTTTCCTACGCAGAATTATGCTAGGTGGTCGAGATTCATTGTAGA
ACTTTAGCCACTACCAATAATGAATC
Found at i:104266809 original size:10 final size:9
Alignment explanation
Indices: 104266796--104266820 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
104266786 CACTAAAACC
104266796 AAAAAAAAT
1 AAAAAAAAT
104266805 AAAAAAAAT
1 AAAAAAAAT
104266814 AAAAAAA
1 AAAAAAA
104266821 GCTTATCCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:104269775 original size:75 final size:74
Alignment explanation
Indices: 104269678--104269944 Score: 408
Period size: 75 Copynumber: 3.6 Consensus size: 74
104269668 ATGGGAACTG
* * * * * *
104269678 GGGTGCTGACCTAACTGTCTCTCTTGTATTCTGGCCCATATTTTGTGGTGGCTGTCGTGGCGTAT
1 GGGTTCTGACCTGACTGACTCTCTTGTATTCTGGCCCATATTTTGAGGTGG-TGTCGTGGTGGAT
104269743 TTTGGAACCA
65 TTTGGAACCA
* *
104269753 GGATTCTGACCTGACTGACTCTCTTGTATTCTGGCCCATATTTTGAGGTGGTTTCCGTGGTGGAT
1 GGGTTCTGACCTGACTGACTCTCTTGTATTCTGGCCCATATTTTGAGGTGGTGT-CGTGGTGGAT
104269818 TTTGGAACCA
65 TTTGGAACCA
* *
104269828 GGGTTCTGACCTGACTGACTCTCTTGTATCCTGGCCCATATTTTGAGGTGGTTGCCGTGGTGGAT
1 GGGTTCTGACCTGACTGACTCTCTTGTATTCTGGCCCATATTTTGAGGTGG-TGTCGTGGTGGAT
104269893 TTTGGAACCA
65 TTTGGAACCA
*
104269903 GGGTTCTGACCTGACTGACTCTCTTGTACTCTGGCCCATATT
1 GGGTTCTGACCTGACTGACTCTCTTGTATTCTGGCCCATATT
104269945 AGGTTGTTCC
Statistics
Matches: 176, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
74 2 0.01
75 173 0.98
76 1 0.01
ACGTcount: A:0.15, C:0.22, G:0.27, T:0.36
Consensus pattern (74 bp):
GGGTTCTGACCTGACTGACTCTCTTGTATTCTGGCCCATATTTTGAGGTGGTGTCGTGGTGGATT
TTGGAACCA
Found at i:104273897 original size:13 final size:13
Alignment explanation
Indices: 104273869--104273916 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
104273859 AAAAATCCAT
104273869 ATATTTTATGTTTAA
1 ATATTTT-T-TTTAA
104273884 ATATTTTTTTTAA
1 ATATTTTTTTTAA
* *
104273897 ATAATTATGTTTAA
1 AT-ATTTTTTTTAA
104273911 ATATTT
1 ATATTT
104273917 ACTTGACTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 10 0.34
14 12 0.41
15 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (13 bp):
ATATTTTTTTTAA
Found at i:104273911 original size:14 final size:14
Alignment explanation
Indices: 104273874--104273913 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
104273864 TCCATATATT
104273874 TTATGTTTAAAT-A
1 TTATGTTTAAATAA
* *
104273887 TTTTTTTTAAATAA
1 TTATGTTTAAATAA
104273901 TTATGTTTAAATA
1 TTATGTTTAAATA
104273914 TTTACTTGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (14 bp):
TTATGTTTAAATAA
Found at i:104280079 original size:10 final size:9
Alignment explanation
Indices: 104280066--104280117 Score: 52
Period size: 9 Copynumber: 5.7 Consensus size: 9
104280056 ATATTTCATA
104280066 AAAAAAATT
1 AAAAAAATT
*
104280075 AAAAAGA-T
1 AAAAAAATT
104280083 AAAAAAATT
1 AAAAAAATT
*
104280092 CAAAAAAGTTT
1 -AAAAAA-ATT
*
104280103 ATAAAAATT
1 AAAAAAATT
104280112 AAAAAA
1 AAAAAA
104280118 CATATTTCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
8 7 0.21
9 14 0.41
10 11 0.32
11 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.21
Consensus pattern (9 bp):
AAAAAAATT
Found at i:104280086 original size:18 final size:17
Alignment explanation
Indices: 104280066--104280116 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 17
104280056 ATATTTCATA
104280066 AAAAAAATTAAAAAGAT
1 AAAAAAATTAAAAAGAT
*
104280083 AAAAAAATTCAAAAAAGTTT
1 AAAAAAATT--AAAAAG-AT
*
104280103 ATAAAAATTAAAAA
1 AAAAAAATTAAAAA
104280117 ACATATTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 9 0.31
18 5 0.17
19 6 0.21
20 9 0.31
ACGTcount: A:0.73, C:0.02, G:0.04, T:0.22
Consensus pattern (17 bp):
AAAAAAATTAAAAAGAT
Found at i:104280354 original size:25 final size:24
Alignment explanation
Indices: 104280307--104280354 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 24
104280297 TTACGCCCTC
*
104280307 TTTTCATATAAAATTATTATTTAT
1 TTTTCATATAAAAATATTATTTAT
104280331 TTTTCATAATAAAAAATATT-TTTA
1 TTTTCAT-AT-AAAAATATTATTTA
104280355 GGAAATTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 7 0.33
25 6 0.29
26 8 0.38
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTCATATAAAAATATTATTTAT
Found at i:104280592 original size:13 final size:13
Alignment explanation
Indices: 104280574--104280599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
104280564 TAATTGAAAT
104280574 GAAAAAAAAAACA
1 GAAAAAAAAAACA
104280587 GAAAAAAAAAACA
1 GAAAAAAAAAACA
104280600 ATCTCCATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (13 bp):
GAAAAAAAAAACA
Found at i:104280880 original size:24 final size:23
Alignment explanation
Indices: 104280852--104280897 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
104280842 ATATTATTTA
*
104280852 TTTATCTAAGTAAAAATAAAATAT
1 TTTATATAAGTAAAAA-AAAATAT
* *
104280876 TTTATATAATTTAAAAAAAATA
1 TTTATATAAGTAAAAAAAAATA
104280898 GTTATTCAAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTATATAAGTAAAAAAAAATAT
Done.