Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009462.1 Hibiscus syriacus cultivar Beakdansim tig00113725_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: 20687664
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 46 of 91
Found at i:9616534 original size:24 final size:25
Alignment explanation
Indices: 9616501--9616560 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
9616491 GTAATATAAT
*
9616501 AATAATAATAAAATAAATAAAG-AA
1 AATAAAAATAAAATAAATAAAGAAA
**
9616525 AATAAAAAT-AAATAAATTGAGTAAA
1 AATAAAAATAAAATAAATAAAG-AAA
9616550 AATAAAAATAA
1 AATAAAAATAA
9616561 TAAGAATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 10 0.33
24 8 0.27
25 11 0.37
26 1 0.03
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (25 bp):
AATAAAAATAAAATAAATAAAGAAA
Found at i:9616575 original size:25 final size:25
Alignment explanation
Indices: 9616501--9616576 Score: 68
Period size: 25 Copynumber: 3.1 Consensus size: 25
9616491 GTAATATAAT
* *
9616501 AATAATAATAAA-ATAAAT-AAAGAA
1 AATAAAAATAAATA-AAATGAAAAAA
* **
9616525 AATAAAAATAAATAAATTGAGTAAA
1 AATAAAAATAAATAAAATGAAAAAA
9616550 AATAAAAAT-AATAAGAATGAAAAAA
1 AATAAAAATAAATAA-AATGAAAAAA
9616575 AA
1 AA
9616577 ATGAAGAGAG
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
24 19 0.46
25 22 0.54
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (25 bp):
AATAAAAATAAATAAAATGAAAAAA
Found at i:9616777 original size:13 final size:13
Alignment explanation
Indices: 9616759--9616784 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
9616749 AAGTATGTAT
9616759 AAAATTAGAAATA
1 AAAATTAGAAATA
9616772 AAAATTAGAAATA
1 AAAATTAGAAATA
9616785 CTAAAAATAA
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:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAATTAGAAATA
Found at i:9619432 original size:2 final size:2
Alignment explanation
Indices: 9619425--9619472 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
9619415 AGTTATTTTC
9619425 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
9619466 AT CT AT A
1 AT AT AT A
9619473 GTTATTCTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9632625 original size:23 final size:22
Alignment explanation
Indices: 9632558--9632638 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
9632548 AGAATGTCCT
*
9632558 GAAGGACCACATA-GATATCCC
1 GAAGGACCACGTAGGATATCCC
* *
9632579 GAAGGACCGCGTA-GAAATGACCC
1 GAAGGACCACGTAGGATAT--CCC
*
9632602 GAAGGACCACGTAGGATTTTCCC
1 GAAGGACCACGTAGGA-TATCCC
*
9632625 GAAGGACCATGTAG
1 GAAGGACCACGTAG
9632639 AACCCTCGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
21 15 0.31
23 31 0.63
24 2 0.04
25 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.27, T:0.15
Consensus pattern (22 bp):
GAAGGACCACGTAGGATATCCC
Found at i:9639769 original size:31 final size:31
Alignment explanation
Indices: 9639725--9639784 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
9639715 TCACAATTCA
9639725 CATAACTTATATCACATAG-GCATGTAACCT
1 CATAACTTATATCACATAGCGCATGTAACCT
* *
9639755 CATAGCTTATTATCACATAGCTCATGTAAC
1 CATAACTTA-TATCACATAGCGCATGTAAC
9639785 ATTCTCATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 8 0.31
31 10 0.38
32 8 0.31
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (31 bp):
CATAACTTATATCACATAGCGCATGTAACCT
Found at i:9665228 original size:19 final size:21
Alignment explanation
Indices: 9665204--9665257 Score: 76
Period size: 19 Copynumber: 2.6 Consensus size: 21
9665194 CGCAAAAATG
9665204 GTATCGATACCATA-ATAG-A
1 GTATCGATACCATAGATAGTA
9665223 GTATCGATACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
*
9665245 GTAACGATACCAT
1 GTATCGATACCAT
9665258 GGTGGTGGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 14 0.45
21 4 0.13
22 13 0.42
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:9665252 original size:22 final size:19
Alignment explanation
Indices: 9665208--9665257 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 19
9665198 AAAATGGTAT
*
9665208 CGATACCATAATAGAGTAT
1 CGATACCATAATAGAGTAA
9665227 CGATACCATAGTATAGTAGTAA
1 CGATACCATA--ATAG-AGTAA
9665249 CGATACCAT
1 CGATACCAT
9665258 GGTGGTGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 10 0.37
21 4 0.15
22 13 0.48
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (19 bp):
CGATACCATAATAGAGTAA
Found at i:9665699 original size:55 final size:56
Alignment explanation
Indices: 9665612--9665795 Score: 207
Period size: 55 Copynumber: 3.3 Consensus size: 56
9665602 TGAGTATGCA
*
9665612 AAAATCTAAGAAATTCATACTAA-T-AGTATGAATTTCTGTATGGCCACTATGTGTGC
1 AAAA-CTAAGAAATTCATACTAAGTGA-TATGAATTTCTGTATGGCCACTATGTGTAC
* *
9665668 AAAACTAAGAAATTCATACTAAGTGAT-TGAATTTCTGTATGGGCACTATTTGTAC
1 AAAACTAAGAAATTCATACTAAGTGATATGAATTTCTGTATGGCCACTATGTGTAC
* * * ** * *
9665723 AGAACTAAGAAATTCATATTAAGTG-TATAAATTTCTGTATGGGAAATATATGTAC
1 AAAACTAAGAAATTCATACTAAGTGATATGAATTTCTGTATGGCCACTATGTGTAC
*
9665778 AAATA-TAAGAAGTTCATA
1 AAA-ACTAAGAAATTCATA
9665796 ATAATTAGGT
Statistics
Matches: 113, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
54 1 0.01
55 104 0.92
56 7 0.06
57 1 0.01
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.34
Consensus pattern (56 bp):
AAAACTAAGAAATTCATACTAAGTGATATGAATTTCTGTATGGCCACTATGTGTAC
Found at i:9665811 original size:110 final size:110
Alignment explanation
Indices: 9665617--9665817 Score: 246
Period size: 110 Copynumber: 1.8 Consensus size: 110
9665607 ATGCAAAAAT
* * * * *
9665617 CTAAGAAATTCATACTAATAGTATGAATTTCTGTATGGCCACTATGTGTGCAAAACTAAGAAATT
1 CTAAGAAATTCATACTAATAGTATAAATTTCTGTATGGCAAATATATGTACAAAACTAAGAAATT
* *
9665682 CATACTAAGTGATTGAATTTCTGTATGGGCACTATTTGTACAGAA
66 CATAATAAGTGATTGAATTTCCGTATGGGCACTATTTGTACAGAA
* * *
9665727 CTAAGAAATTCATATTAAGT-GTATAAATTTCTGTATGGGAAATATATGTACAAATA-TAAGAAG
1 CTAAGAAATTCATACTAA-TAGTATAAATTTCTGTATGGCAAATATATGTACAAA-ACTAAGAAA
* *
9665790 TTCATAATAATTAGGTT-AATTTCCGTAT
64 TTCATAATAAGT-GATTGAATTTCCGTAT
9665818 TAGTAGTGGG
Statistics
Matches: 76, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
110 71 0.93
111 5 0.07
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (110 bp):
CTAAGAAATTCATACTAATAGTATAAATTTCTGTATGGCAAATATATGTACAAAACTAAGAAATT
CATAATAAGTGATTGAATTTCCGTATGGGCACTATTTGTACAGAA
Found at i:9666096 original size:68 final size:68
Alignment explanation
Indices: 9665979--9666517 Score: 705
Period size: 68 Copynumber: 8.0 Consensus size: 68
9665969 CAAGATTAAT
* * *
9665979 GGCCTAAATGTGCATTTGAAAGAAAGGTGTCAATCATGCCAGTTTGATGAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
9666044 TGA
66 TGA
* * * * **
9666047 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATACAAGTTAGATGAAAGGCAAAATATCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
*
9666112 TCA
66 TGA
*
9666115 GGCCTAACTGTGCATTTGATAGAAAGGTGTCAATCATGCCAGTT--A-G--AGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
*
9666175 TAA
66 TGA
* * * * * * *
9666178 GGCTTAACTGTGCATTTGATAGAAAGGTGACAATTATGGCAGATAGATGAAAGGCTAAGTGCATT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
9666243 TGA
66 TGA
* * * * *
9666246 GGCCTAACTATGAATTTGACAGAAAGGTGTCAATTATGCCATTTAGATAAAAGGCTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
9666311 TGA
66 TGA
9666314 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCA-TCTAGATGAAAGGCTAAGTGCCT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGT-TAGATGAAAGGCTAAGTGCCT
9666378 TTGA
65 TTGA
* * * *
9666382 GGCCTAACTGTGCATTTTATATAAAGGTGTCAATGATGCCAGTTAGATGAAAGGCTAAGTGCC-T
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
9666446 TGA
66 TGA
* * * * * * *
9666449 GGCCTGACTGTGCATTTGACAGGAAGGTGTCAATGATACCAGTTAGATGAAAGGTTAAATACCTT
1 GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
9666514 TGA
66 TGA
9666517 G
1 G
9666518 TAAAAGATTA
Statistics
Matches: 411, Mismatches: 52, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
63 51 0.12
65 2 0.00
66 2 0.00
67 59 0.14
68 296 0.72
69 1 0.00
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.28
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGCTAAGTGCCTT
TGA
Found at i:9666608 original size:45 final size:45
Alignment explanation
Indices: 9666560--9666898 Score: 484
Period size: 45 Copynumber: 7.5 Consensus size: 45
9666550 GTATAAAAGG
9666560 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATC-A
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGA
* *
9666604 GCATGAAATGG-TGCCATAATTAAAATGCATATGGGTGCATTATCGG
1 -CATGAAA-GGATGCCATAATTGAAATGCATATGGGTGCATTATCGA
* * *
9666650 CATGAAAGGTTGCCCTAATTGAAATGCATATGGTTGCATTATCGA
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGA
9666695 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGA
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGA
* * * *
9666740 CATGAAATGATTCCATAATTGAAATGCATATGGGTGCATTATTGG
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGA
* *
9666785 CATGAAAAGATGCCATAATTGAAATGCATATGGGTGTATTATCGA
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGA
* * *
9666830 CATGAAAGGATGCCATAGTTTAAATGCATATGGGTGTATTATCGA
1 CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGA
* * * *
9666875 TATGAAAAGATGCTATAAATGAAA
1 CATGAAAGGATGCCATAATTGAAA
9666899 AGGCATAATG
Statistics
Matches: 264, Mismatches: 27, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
44 2 0.01
45 260 0.98
46 2 0.01
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (45 bp):
CATGAAAGGATGCCATAATTGAAATGCATATGGGTGCATTATCGA
Found at i:9678666 original size:23 final size:23
Alignment explanation
Indices: 9678598--9678666 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
9678588 CAACCTTATA
*
9678598 TGGCACTTCAGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* * * *
9678621 CGGCACTACGATGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
* *
9678644 TGGCACTTTGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTCTACG
9678667 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:9682174 original size:24 final size:23
Alignment explanation
Indices: 9682146--9682211 Score: 68
Period size: 24 Copynumber: 3.0 Consensus size: 23
9682136 GCATCGATGC
9682146 TTAAGGAGTGCATCGATGCACATG
1 TTAAGGAGTGCATCGATGCAC-TG
*
9682170 TTAAGG-GATGCATCGATACACTG
1 TTAAGGAG-TGCATCGATGCACTG
*
9682193 -T-A-GAATGCATCGATGCACT
1 TTAAGGAGTGCATCGATGCACT
9682212 TGAAGGGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 14 0.38
21 1 0.03
22 1 0.03
23 3 0.08
24 18 0.49
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (23 bp):
TTAAGGAGTGCATCGATGCACTG
Found at i:9683033 original size:23 final size:23
Alignment explanation
Indices: 9682976--9683036 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
9682966 CAACCTTATA
* *
9682976 TGGCATTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* * * *
9682999 CGGAACTACGGTGCAATTCTATG
1 TGGCACTTCGGTGCAATTCTACG
9683022 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
9683037 TTTATACGAG
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.18, C:0.23, G:0.28, T:0.31
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:9686560 original size:2 final size:2
Alignment explanation
Indices: 9686553--9686582 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9686543 TCATAAACCC
9686553 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
9686583 TAACTCTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9694696 original size:54 final size:54
Alignment explanation
Indices: 9694648--9694801 Score: 227
Period size: 54 Copynumber: 2.9 Consensus size: 54
9694638 CAATACAGTT
*
9694648 ATTCATAAACTTATTATGAATTTCTTAGTTTGTACACACAGTGCCAATACGGAA
1 ATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGGAA
* * * *
9694702 ATTCATAAACCTATTATTAATTTTTTAGGTTGCACACACAGTGCCAATACGGAA
1 ATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGGAA
* * * *
9694756 ATTTATAAACTTATTATGAATTTCTTAATTTGCACGCATAGTGCCA
1 ATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCA
9694802 TTCGGTAATC
Statistics
Matches: 87, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 87 1.00
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.36
Consensus pattern (54 bp):
ATTCATAAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGGAA
Found at i:9695236 original size:18 final size:19
Alignment explanation
Indices: 9695194--9695241 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
9695184 ATAATCAATG
**
9695194 GTATCGATACCTTCCTCATA
1 GTATCGATACCCACCTCA-A
9695214 GTATCGATACCCACCTC-A
1 GTATCGATACCCACCTCAA
9695232 GTATCGATAC
1 GTATCGATAC
9695242 TAATTGCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
20 15 0.58
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.29
Consensus pattern (19 bp):
GTATCGATACCCACCTCAA
Found at i:9699881 original size:24 final size:25
Alignment explanation
Indices: 9699847--9699905 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
9699837 ATCATAATAT
* *
9699847 AATCCAAGTCAAGT-ATTAGAA-CAG
1 AATCCAGGTCAAGTCATCA-AATCAG
9699871 AATCCAGGTC-AGTCATCAAATCAG
1 AATCCAGGTCAAGTCATCAAATCAG
9699895 AATCCAGGTCA
1 AATCCAGGTCA
9699906 GAAATCAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 5 0.17
24 25 0.83
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (25 bp):
AATCCAGGTCAAGTCATCAAATCAG
Found at i:9704981 original size:54 final size:54
Alignment explanation
Indices: 9704915--9705213 Score: 490
Period size: 54 Copynumber: 5.5 Consensus size: 54
9704905 TAATTTCCCC
9704915 AAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGGAAATTCAT
1 AAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGGAAATTCAT
* * * *
9704969 AAACTTATTATGAATTTCTTAGCTTGCACACACAATTCCAATATGGAAATTCAT
1 AAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGGAAATTCAT
* * *
9705023 AAACTTATTATGAATTTCTTAGTTTGAACACACAGTGCCGATACGAAAATTCAT
1 AAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGGAAATTCAT
*
9705077 AAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGAAAATTCAT
1 AAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGGAAATTCAT
* * *
9705131 AAACTTATTATGATTTTCTTAGTTTGTACACACAATGCCAATACGGAAATTCAT
1 AAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGGAAATTCAT
*
9705185 AAACTTATTATGAATTTCTAAGTTTGCAC
1 AAACTTATTATGAATTTCTTAGTTTGCAC
9705214 GCATATTTCC
Statistics
Matches: 225, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 225 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (54 bp):
AAACTTATTATGAATTTCTTAGTTTGCACACACAGTGCCAATACGGAAATTCAT
Found at i:9706989 original size:3 final size:3
Alignment explanation
Indices: 9706981--9707083 Score: 89
Period size: 3 Copynumber: 33.3 Consensus size: 3
9706971 TGTCCAAAAT
* * * * * * *
9706981 TTA TTA TTA TTA TTA GTA TTA TTA TTG TTG TTG TTC TTC TTC TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* **
9707029 TTA TTA GTTA TTG TTA TTA TTAA TTA TTA TTA TTAA CAA TTA TTA TTA
1 TTA TTA -TTA TTA TTA TTA TT-A TTA TTA TTA TT-A TTA TTA TTA TTA
9707077 TTA TTA T
1 TTA TTA T
9707084 AAGTAAAATA
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
3 79 0.92
4 7 0.08
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:9707047 original size:16 final size:16
Alignment explanation
Indices: 9707023--9707082 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
9707013 GTTCTTCTTC
*
9707023 TTATTATTATTAGTTA
1 TTATTATTATTAATTA
*
9707039 TTGTTATTATTAATTA
1 TTATTATTATTAATTA
**
9707055 TTATTATTAACAATTA
1 TTATTATTATTAATTA
9707071 TTATTATTATTA
1 TTATTATTATTA
9707083 TAAGTAAAAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (16 bp):
TTATTATTATTAATTA
Found at i:9708379 original size:24 final size:24
Alignment explanation
Indices: 9708334--9708396 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
9708324 TCACTCCAAG
**
9708334 AATCAACCCTTGGTTTGAATGATTA
1 AATCAA-CCTTGAATTGAATGATTA
*
9708359 AATCAACCTTGAATTGGATGATTA
1 AATCAACCTTGAATTGAATGATTA
* *
9708383 AATCAGCATTGAAT
1 AATCAACCTTGAAT
9708397 GCTTTGAATT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 27 0.82
25 6 0.18
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (24 bp):
AATCAACCTTGAATTGAATGATTA
Found at i:9712158 original size:408 final size:408
Alignment explanation
Indices: 9711403--9712218 Score: 1488
Period size: 408 Copynumber: 2.0 Consensus size: 408
9711393 CGATAGGATG
9711403 AAATAGCCAATAGGGGGTGAATTGGCAATTAAAATTTTGGTGGAAGTTGTTTGGAGCGTATGGGT
1 AAATAGCCAATAGGGGGTGAATTGGCAATTAAAATTTTGGTGGAAGTTGTTTGGAGCGTATGGGT
*
9711468 ATCGGTACTCCTCCATAGGGGTATCGATACTACTTGTATAAAATTCAAATATTTCGACCGTTGCA
66 ATCGGTACTCCTCCATAGGGGTATCGATACTACCTGTATAAAATTCAAATATTTCGACCGTTGCA
* * *
9711533 AACTCAGTGGTATCGATACCTCTCAAGGGTGTATCAATACTACTATGTAAAGAGGTATTGATATC
131 AACTCAATGGTATCGATACCTCTCAAGGGTGTATCAATACTACTATGTAAAGAGGTATCGATACC
9711598 AGTCATGGTATCGGTACCCATTTTGCATTATGTTATTTCTCGGAGTCAAAATCAAAAGGGGTAGT
196 AGTCATGGTATCGGTACCCATTTTGCATTATGTTATTTCTCGGAGTCAAAATCAAAAGGGGTAGT
* *
9711663 ATCGGTATCTATGATAGGTATCGGTACTACTATATATAGGGGTATTGATACCCTGTAGGGTATCA
261 ATCGGTATCTATGATAGGTATCGATACTACTATATATAGGGGTATCGATACCCTGTAGGGTATCA
9711728 ATACCTCTTTTGCATTCGATGTTTGAGGGGTATCGATACTCGTTAAGAAGGTATCGATACTTCCC
326 ATACCTCTTTTGCATTCGATGTTTGAGGGGTATCGATACTCGTTAAGAAGGTATCGATACTTCCC
9711793 TATTTAAAACACAATTTT
391 TATTTAAAACACAATTTT
9711811 AAATAGCCAATAGGGGGTGAATTGGCAATTAAAATTTTGGTGGAAGTTGTTTGGAGCGTATGGGT
1 AAATAGCCAATAGGGGGTGAATTGGCAATTAAAATTTTGGTGGAAGTTGTTTGGAGCGTATGGGT
*
9711876 ATCGGTACTCCTCCATAGGGGTATCGATAGTACCTGTATAAAATTCAAATATTTCGACCGTTGCA
66 ATCGGTACTCCTCCATAGGGGTATCGATACTACCTGTATAAAATTCAAATATTTCGACCGTTGCA
*
9711941 AACTCAATGGTATCGATACCTCTCAAGGGTGTATCAATACTACTTTGTAAAGAGGTATCGATACC
131 AACTCAATGGTATCGATACCTCTCAAGGGTGTATCAATACTACTATGTAAAGAGGTATCGATACC
* * * *
9712006 GGTCATGGTATCGGTACCCATTTTGCATTCTGTTATTTCTTGGAGTCAAAATCAAAAGGGGTGGT
196 AGTCATGGTATCGGTACCCATTTTGCATTATGTTATTTCTCGGAGTCAAAATCAAAAGGGGTAGT
* *
9712071 ATTGGTATCTATGATAGGTATCGATACTACTATATATAGGGGTATCGATACCCTGTAGGGTATCC
261 ATCGGTATCTATGATAGGTATCGATACTACTATATATAGGGGTATCGATACCCTGTAGGGTATCA
* *
9712136 ATACCTCTTTTGTATTCGATGTTTGAGGGGTATCGATACTCGTTAAGAATGTATCGATACTTCCC
326 ATACCTCTTTTGCATTCGATGTTTGAGGGGTATCGATACTCGTTAAGAAGGTATCGATACTTCCC
9712201 TATTTAAAACACAATTTT
391 TATTTAAAACACAATTTT
9712219 GACTCGATTA
Statistics
Matches: 392, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
408 392 1.00
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (408 bp):
AAATAGCCAATAGGGGGTGAATTGGCAATTAAAATTTTGGTGGAAGTTGTTTGGAGCGTATGGGT
ATCGGTACTCCTCCATAGGGGTATCGATACTACCTGTATAAAATTCAAATATTTCGACCGTTGCA
AACTCAATGGTATCGATACCTCTCAAGGGTGTATCAATACTACTATGTAAAGAGGTATCGATACC
AGTCATGGTATCGGTACCCATTTTGCATTATGTTATTTCTCGGAGTCAAAATCAAAAGGGGTAGT
ATCGGTATCTATGATAGGTATCGATACTACTATATATAGGGGTATCGATACCCTGTAGGGTATCA
ATACCTCTTTTGCATTCGATGTTTGAGGGGTATCGATACTCGTTAAGAAGGTATCGATACTTCCC
TATTTAAAACACAATTTT
Found at i:9713414 original size:3 final size:3
Alignment explanation
Indices: 9713406--9713441 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
9713396 TCATACTAAG
*
9713406 CAA CAA CAA CAA CAA CTA -AA CAA CAA CAA CAA CAA C
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA CAA C
9713442 TAAACATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 1 0.03
3 29 0.97
ACGTcount: A:0.64, C:0.33, G:0.00, T:0.03
Consensus pattern (3 bp):
CAA
Found at i:9713429 original size:20 final size:20
Alignment explanation
Indices: 9713400--9713447 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
9713390 TATCAGTCAT
*
9713400 ACTAAGCAACAACAACAACA
1 ACTAAACAACAACAACAACA
9713420 ACTAAACAACAACAACAACA
1 ACTAAACAACAACAACAACA
9713440 ACTAAACA
1 ACTAAACA
9713448 TTTTCACACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.62, C:0.29, G:0.02, T:0.06
Consensus pattern (20 bp):
ACTAAACAACAACAACAACA
Found at i:9714810 original size:106 final size:109
Alignment explanation
Indices: 9714687--9714911 Score: 309
Period size: 106 Copynumber: 2.1 Consensus size: 109
9714677 TTAATGTATA
*
9714687 TTTTTATTTTCGACGGAATG-TCTATTCCATCACAAATTAAA-TGACTATATTTTAATT-A-AAA
1 TTTTTATTTTCGACGGAATGAT-TATTCAATCACAAATTAAATTGA-TATATTTTAATTAATAAA
*
9714748 A-AATTCCT-ACAGAATCATTGTCCCGTCATAAATTAAATTGATATT
64 ACAATT-CTGACAGAATCATTGTCCCGTCATAAATTAAATTAATATT
9714793 TTTTTATTTTCGACGGAATGATTATTCAATCACAAATTAAATTGATATATTTTAATTAAAATTGA
1 TTTTTATTTTCGACGGAATGATTATTCAATCACAAATTAAATTGATATATTTTAATT--AA-T-A
* *
9714858 AAACAATTTTGACGGAATCATTGTCCCGTCATAAATTAAATTAATATT
62 AAACAATTCTGACAGAATCATTGTCCCGTCATAAATTAAATTAATATT
9714906 TTTTTA
1 TTTTTA
9714912 CTTAAATGAA
Statistics
Matches: 105, Mismatches: 4, Indels: 13
0.86 0.03 0.11
Matches are distributed among these distances:
106 50 0.48
107 4 0.04
109 1 0.01
112 5 0.05
113 45 0.43
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.41
Consensus pattern (109 bp):
TTTTTATTTTCGACGGAATGATTATTCAATCACAAATTAAATTGATATATTTTAATTAATAAAAC
AATTCTGACAGAATCATTGTCCCGTCATAAATTAAATTAATATT
Found at i:9716384 original size:16 final size:17
Alignment explanation
Indices: 9716363--9716396 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
9716353 ACAAATTTAT
*
9716363 AAAATTTTTGA-AAAAA
1 AAAATTATTGATAAAAA
9716379 AAAATTATTGATAAAAA
1 AAAATTATTGATAAAAA
9716396 A
1 A
9716397 TAAAAAACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
AAAATTATTGATAAAAA
Found at i:9722605 original size:22 final size:20
Alignment explanation
Indices: 9722554--9722626 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
9722544 ATCTAATTTT
9722554 GGTATCGATA-CCAGTAAGG
1 GGTATCGATACCCAGTAAGG
*
9722573 GGTATCAATACCCTAGT-AGG
1 GGTATCGATACCC-AGTAAGG
9722593 GTAGTATCGATA-CCATGGTAA-G
1 G--GTATCGATACCCA--GTAAGG
9722615 GGTATCGATACC
1 GGTATCGATACC
9722627 AAGCAATATC
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
19 9 0.20
20 16 0.36
21 6 0.14
22 12 0.27
23 1 0.02
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCCAGTAAGG
Found at i:9722621 original size:20 final size:19
Alignment explanation
Indices: 9722554--9722627 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 19
9722544 ATCTAATTTT
9722554 GGTATCGATACCA-GTAAGG
1 GGTATCGATACCATGTAA-G
* * *
9722573 GGTATCAATACCCTAGTAGG
1 GGTATCGATACCAT-GTAAG
9722593 GTAGTATCGATACCATGGTAAG
1 G--GTATCGATACCAT-GTAAG
9722615 GGTATCGATACCA
1 GGTATCGATACCA
9722628 AGCAATATCG
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
19 11 0.25
20 14 0.32
21 3 0.07
22 16 0.36
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (19 bp):
GGTATCGATACCATGTAAG
Found at i:9722670 original size:95 final size:95
Alignment explanation
Indices: 9722506--9722720 Score: 227
Period size: 95 Copynumber: 2.3 Consensus size: 95
9722496 GGTAGTTTAA
* * * * *
9722506 ATACCATGATAAGGGGTATCAATTCCAAGAAAAATCGAATCTAATTTTGGTATCGATACCAGTAA
1 ATACCATGGTAA-GGGTATCGATACCAAGAAAAATCGAACCTAATTTTGGAATCGATACCAGTAA
* * *
9722571 GGGGTATCAATACCCTAGTAGGGTAGTATCG
65 GGGGTATCAATACCATAGTAGAGAAGTATCG
* * * * *
9722602 ATACCATGGTAAGGGTATCGATACCAAGCAATATCGAACCTATTTTTGGAATCGATACCCG-AGG
1 ATACCATGGTAAGGGTATCGATACCAAGAAAAATCGAACCTAATTTTGGAATCGATACCAGTA-A
** *
9722666 GGGGTATCGGTACCATAGTATAGAAGTATCG
65 GGGGTATCAATACCATAGTAGAGAAGTATCG
* *
9722697 ATACTATGGT-AGTAGTATCGATAC
1 ATACCATGGTAAG-GGTATCGATAC
9722721 TATGGTGCCA
Statistics
Matches: 99, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
94 3 0.03
95 85 0.86
96 11 0.11
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.27
Consensus pattern (95 bp):
ATACCATGGTAAGGGTATCGATACCAAGAAAAATCGAACCTAATTTTGGAATCGATACCAGTAAG
GGGTATCAATACCATAGTAGAGAAGTATCG
Found at i:9723105 original size:58 final size:59
Alignment explanation
Indices: 9723043--9723207 Score: 201
Period size: 59 Copynumber: 2.8 Consensus size: 59
9723033 ACCAAATGGA
* *
9723043 ACTTCGTGTG-TAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGCATAGGGC
1 ACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTACATAGGGC
* * * * *
9723101 ACTTCGTATGCTAACATGATAAGAAATTCATATTAAGTGTATGAATTTCTATATTGGGC
1 ACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTACATAGGGC
* * **
9723160 ACCTT-GTGTGCT-AAAGGATAAGGAATTCATACTAAGCCTATGAATTTC
1 A-CTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTC
9723208 CATATGGGAA
Statistics
Matches: 91, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
58 39 0.43
59 49 0.54
60 3 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (59 bp):
ACTTCGTGTGCTAAAATGATAAGAAATTCATACTAAGTGTATGAATTTCTACATAGGGC
Found at i:9723720 original size:68 final size:68
Alignment explanation
Indices: 9723594--9723720 Score: 164
Period size: 68 Copynumber: 1.9 Consensus size: 68
9723584 GGCCTAACTT
* * ** *
9723594 TGCATATGATAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGACTAAGTGTATTTGAGGGATAA
1 TGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTACAGTTGAGGGATAA
9723659 TTG
66 TTG
* * ** *
9723662 TGCATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGTTGAG
1 TGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTACAGTTGAG
9723721 TAAAAGAATA
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
68 49 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.31
Consensus pattern (68 bp):
TGCATATGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGACTAAGTACAGTTGAGGGATAA
TTG
Found at i:9723801 original size:80 final size:80
Alignment explanation
Indices: 9723660--9724050 Score: 527
Period size: 80 Copynumber: 4.9 Consensus size: 80
9723650 GAGGGATAAT
* * * * * *
9723660 TGTGCATATGACATAAAGGTGTCAATTATGCCAGTTAGATGAATGGTTAAGTACCGTTGAGTAAA
1 TGTGCAT-TGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACTGTTGAGTAAA
9723725 AGAATAATGGCCTAAC
65 AGAATAATGGCCTAAC
* * * * *
9723741 TGTGCATTGACAGAAATATGTCAATTACGCCAGCTAGGTGAACGATTAAGTACTGTTGAGTAAAA
1 TGTGCATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACTGTTGAGTAAAA
9723806 GAATAATGGCCTAAC
66 GAATAATGGCCTAAC
* * * *
9723821 AGTGAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAGTA-TCGTTAAGTAAA
1 TGTGCATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACT-GTTGAGTAAA
9723885 AGAATAATGGCCTAAC
65 AGAATAATGGCCTAAC
* * *
9723901 TGTGCATTGGTAGAAATGTGTCAATTATGCCAGTTAGATTAACGGTTAAGTAGC-GTTGAGTAAA
1 TGTGCATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAGTA-CTGTTGAGTAAA
9723965 AGAATAATGGCCTAAC
65 AGAATAATGGCCTAAC
* * ** *
9723981 TGTGCATTGGCAGAAATGTGTTAATTATGCCAGTTAGACGAACG-TTAAACACTGTTGAGTAAGA
1 TGTGCATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACTGTTGAGTAAAA
9724045 GAATAA
66 GAATAA
9724051 AGAAATTTTA
Statistics
Matches: 274, Mismatches: 32, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
78 1 0.00
79 22 0.08
80 244 0.89
81 7 0.03
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (80 bp):
TGTGCATTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACTGTTGAGTAAAA
GAATAATGGCCTAAC
Found at i:9724090 original size:2 final size:2
Alignment explanation
Indices: 9724083--9724150 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
9724073 TGAAGGGATG
9724083 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9724125 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
9724151 GTAAAACAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9727208 original size:25 final size:26
Alignment explanation
Indices: 9727163--9727217 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
9727153 TGTCTCCCTC
* *
9727163 TTTAAACTTTTTCTTTCTTTTG-TTT
1 TTTAAAATTTTTATTTCTTTTGATTT
9727188 TTTAAAATTATTTATTT-TTTTGATTT
1 TTTAAAATT-TTTATTTCTTTTGATTT
9727214 TTTA
1 TTTA
9727218 CTAATCTAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 13 0.50
26 13 0.50
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (26 bp):
TTTAAAATTTTTATTTCTTTTGATTT
Found at i:9728069 original size:21 final size:21
Alignment explanation
Indices: 9728030--9728088 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
9728020 GAATTAAATC
*
9728030 ACCCTTGAA-TAATATGAACA
1 ACCCTTGAATTTATATGAACA
*
9728050 ACCCTTGAATTTAGATGAACA
1 ACCCTTGAATTTATATGAACA
9728071 ACCCTTGAATTTATATGA
1 ACCCTTGAATTTATATGA
9728089 TAAAAATAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
20 9 0.26
21 26 0.74
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.31
Consensus pattern (21 bp):
ACCCTTGAATTTATATGAACA
Found at i:9728579 original size:17 final size:17
Alignment explanation
Indices: 9728504--9728570 Score: 80
Period size: 17 Copynumber: 3.9 Consensus size: 17
9728494 AAGAGTTAGT
* * *
9728504 TTAATAAATGAACTCGT
1 TTAATTAATGAACTAGG
* *
9728521 TTGATGAATGAACTAGG
1 TTAATTAATGAACTAGG
*
9728538 CTAATTAATGAACTAGG
1 TTAATTAATGAACTAGG
9728555 TTAATTAATGAACTAG
1 TTAATTAATGAACTAG
9728571 ATTATTTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.40, C:0.09, G:0.18, T:0.33
Consensus pattern (17 bp):
TTAATTAATGAACTAGG
Found at i:9730301 original size:18 final size:18
Alignment explanation
Indices: 9730259--9730305 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
9730249 TAGTTTAGTA
*
9730259 AATGAACTA-CTTTAATT
1 AATGAACTAGATTTAATT
*
9730276 AATAAACTAGATTT-ATT
1 AATGAACTAGATTTAATT
9730293 CAATGAACTAGAT
1 -AATGAACTAGAT
9730306 GCATAAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAGATTTAATT
Found at i:9730316 original size:17 final size:17
Alignment explanation
Indices: 9730294--9730377 Score: 53
Period size: 17 Copynumber: 4.8 Consensus size: 17
9730284 AGATTTATTC
9730294 AATGAACTAGATGCATA
1 AATGAACTAGATGCATA
* * *
9730311 AATGAAGTAGCT-TACTA
1 AATGAACTAGATGCA-TA
* *
9730328 AATGATCTAAATATGCATA
1 AATGAACT--AGATGCATA
** * *
9730347 AATGAACTACTTCCTTA
1 AATGAACTAGATGCATA
9730364 AATGAACTAGATGC
1 AATGAACTAGATGC
9730378 TTTAAATGCA
Statistics
Matches: 47, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
16 1 0.02
17 34 0.72
19 11 0.23
20 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (17 bp):
AATGAACTAGATGCATA
Found at i:9731033 original size:18 final size:18
Alignment explanation
Indices: 9731012--9731053 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
9731002 GTTGTTTTTA
**
9731012 AAATAAAAGATGAGAATT
1 AAATAAAAGAAAAGAATT
*
9731030 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
9731048 AAATAA
1 AAATAA
9731054 TCAAATTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:9731668 original size:70 final size:73
Alignment explanation
Indices: 9731592--9731779 Score: 274
Period size: 75 Copynumber: 2.6 Consensus size: 73
9731582 TAAAACATCT
* * * *
9731592 TAAATCCTAATTAAAACACTAAAAACTATTTAAACTAAAATACCT-A-AAA-ATAATATTTAAAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAACAAAGATAAAATATAAAA
*
9731654 TAATATTC
66 TAATATCC
9731662 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCT--AACAAAGATAAAATATAA
9731727 AATAATATCC
64 AATAATATCC
* *
9731737 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
1 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATAC
9731780 AAAGATAAAA
Statistics
Matches: 106, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
70 43 0.41
73 1 0.01
74 3 0.03
75 59 0.56
ACGTcount: A:0.56, C:0.14, G:0.01, T:0.29
Consensus pattern (73 bp):
TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAACAAAGATAAAATATAAAA
TAATATCC
Found at i:9731689 original size:19 final size:19
Alignment explanation
Indices: 9731661--9731770 Score: 57
Period size: 19 Copynumber: 5.8 Consensus size: 19
9731651 AAATAATATT
*
9731661 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* *
9731680 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAAATA
* *
9731699 --AAATACCTAA-AACAAAGA
1 CTAAA-ACCTAATTA-AAATA
** * * *
9731717 -TAAAATATAAAATAATATC
1 CTAAAACCT-AATTAAAATA
*
9731736 CTAAAACTTAATTAAAATA
1 CTAAAACCTAATTAAAATA
*
9731755 CTAAAACCTATTTAAA
1 CTAAAACCTAATTAAA
9731771 CTAAAATACA
Statistics
Matches: 65, Mismatches: 20, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
17 4 0.06
18 10 0.15
19 44 0.68
20 7 0.11
ACGTcount: A:0.56, C:0.15, G:0.01, T:0.28
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:9731803 original size:75 final size:74
Alignment explanation
Indices: 9731592--9731815 Score: 271
Period size: 75 Copynumber: 3.1 Consensus size: 74
9731582 TAAAACATCT
* * * *
9731592 TAAATCCTAATTAAAACACTAAAAACTATTTAAACTAAAATAC---CTAAAA-ATAATATTTAAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAAA
*
9731653 ATAATATTC
66 ATAATATCC
* * *
9731662 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATA-AA-ATAT
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATA-C-AAAATAAA-ATATAATATTT
9731725 AAAATAATATCC
63 AAAATAATATCC
* *
9731737 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAGATAAAATATAATGTTTAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAA-ATAAAATATAATATTTAA
*
9731802 AATATTATCC
65 AATAATATCC
9731812 TAAA
1 TAAA
9731816 CTTGAGTTTA
Statistics
Matches: 132, Mismatches: 12, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
70 40 0.30
71 1 0.01
73 6 0.05
74 7 0.05
75 74 0.56
76 3 0.02
77 1 0.01
ACGTcount: A:0.56, C:0.12, G:0.01, T:0.30
Consensus pattern (74 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACAAAATAAAATATAATATTTAAA
ATAATATCC
Found at i:9733469 original size:5 final size:5
Alignment explanation
Indices: 9733440--9733554 Score: 76
Period size: 5 Copynumber: 22.8 Consensus size: 5
9733430 TGTTTAGGAA
* *
9733440 AAAAT AAAA- AAAA- AAAGT -AATT AAAAT AAAAT -AAAT AAAAT GAAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT
* **** *
9733487 AAATTT TGCTT ACAAAT AAAAT AAAAAT AAAAT AAAAT AAAGTT AAAAT
1 AAA-AT AAAAT A-AAAT AAAAT -AAAAT AAAAT AAAAT AAA-AT AAAAT
*
9733536 AAAAT TAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
9733555 AATATATAAC
Statistics
Matches: 87, Mismatches: 15, Indels: 16
0.74 0.13 0.14
Matches are distributed among these distances:
4 14 0.16
5 56 0.64
6 17 0.20
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:9733563 original size:16 final size:16
Alignment explanation
Indices: 9733500--9733554 Score: 76
Period size: 16 Copynumber: 3.5 Consensus size: 16
9733490 TTTTGCTTAC
9733500 AAATAAAATAAAAATA
1 AAATAAAATAAAAATA
**
9733516 AAATAAAATAAAGTTA
1 AAATAAAATAAAAATA
*
9733532 AAATAAAAT-TAAATA
1 AAATAAAATAAAAATA
9733547 AAATAAAA
1 AAATAAAA
9733555 AATATATAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 11 0.32
16 23 0.68
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (16 bp):
AAATAAAATAAAAATA
Found at i:9739194 original size:18 final size:18
Alignment explanation
Indices: 9739173--9739220 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
9739163 GTTGTTTTTA
* *
9739173 AAATAAAAGATAAGAGTT
1 AAATAAAAAATAAGAATT
*
9739191 AAATAAAAAATAATAATT
1 AAATAAAAAATAAGAATT
9739209 AAATAAACAAAT
1 AAATAAA-AAAT
9739221 TAAAGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (18 bp):
AAATAAAAAATAAGAATT
Found at i:9739697 original size:12 final size:12
Alignment explanation
Indices: 9739682--9739711 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
9739672 AAAAGTATAC
9739682 GAAAAATAGAGA
1 GAAAAATAGAGA
9739694 GAAAAATAGAGA
1 GAAAAATAGAGA
9739706 GAAAAA
1 GAAAAA
9739712 GAAGATTTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.70, C:0.00, G:0.23, T:0.07
Consensus pattern (12 bp):
GAAAAATAGAGA
Found at i:9739906 original size:19 final size:19
Alignment explanation
Indices: 9739878--9739988 Score: 61
Period size: 19 Copynumber: 5.8 Consensus size: 19
9739868 AAATAATATT
*
9739878 CTAAATCCTAATTAAAATA
1 CTAAAACCTAATTAAAATA
* *
9739897 CTAAAACCTATTTAAACTA
1 CTAAAACCTAATTAAAATA
*
9739916 --AAATACCTAA-AACAAATA
1 CTAAA-ACCTAATTA-AAATA
** *
9739934 -TAAAATATAA-AAATAATA
1 CTAAAACCTAATTAA-AATA
*
9739952 TCATAAAACTTAATTAAAATA
1 -C-TAAAACCTAATTAAAATA
*
9739973 CTAAAACCTATTTAAA
1 CTAAAACCTAATTAAA
9739989 CTAAAATACA
Statistics
Matches: 71, Mismatches: 13, Indels: 16
0.71 0.13 0.16
Matches are distributed among these distances:
17 5 0.07
18 19 0.27
19 32 0.45
20 1 0.01
21 12 0.17
22 2 0.03
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.29
Consensus pattern (19 bp):
CTAAAACCTAATTAAAATA
Found at i:9739937 original size:25 final size:24
Alignment explanation
Indices: 9739890--9739937 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
9739880 AAATCCTAAT
** *
9739890 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATATAAAC
9739914 TAAAATACCTAAAACAAATATAAA
1 TAAAATA-CTAAAACAAATATAAA
9739938 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (24 bp):
TAAAATACTAAAACAAATATAAAC
Found at i:9740021 original size:76 final size:77
Alignment explanation
Indices: 9739852--9740021 Score: 224
Period size: 76 Copynumber: 2.2 Consensus size: 77
9739842 CTAAAATCTC
* *
9739852 TAAAAAATAATATTT-AAAATAATATTCTAAATCCTAATTAAAATACTAAAACCTATTTAAACTA
1 TAAAATATAATATTTAAAAATAATATTCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTA
9739916 AAATACCTAAAA
66 AAATACCTAAAA
* * * *
9739928 -CAAATATAAAATATAAAAATAATA-TCATAAAACTTAATTAAAATACTAAAACCTATTTAAACT
1 TAAAATATAATATTTAAAAATAATATTC-TAAAACCTAATTAAAATACTAAAACCTATTTAAACT
9739991 AAAATA-C-AAAGA
65 AAAATACCTAAA-A
*
9740003 TAAAATATAATGTTTAAAA
1 TAAAATATAATATTTAAAA
9740022 TATTATCCTA
Statistics
Matches: 80, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
74 3 0.04
75 14 0.17
76 63 0.79
ACGTcount: A:0.59, C:0.10, G:0.01, T:0.30
Consensus pattern (77 bp):
TAAAATATAATATTTAAAAATAATATTCTAAAACCTAATTAAAATACTAAAACCTATTTAAACTA
AAATACCTAAAA
Found at i:9740712 original size:29 final size:29
Alignment explanation
Indices: 9740670--9740727 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
9740660 AAACGAACAC
*
9740670 AAGTATTGGGACTTCAAGTGATAAATTCT
1 AAGTATTGGGACTTCAAGTGACAAATTCT
9740699 AAGTATTGGGACTTCAAGTGACAAATTCT
1 AAGTATTGGGACTTCAAGTGACAAATTCT
9740728 TTAGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (29 bp):
AAGTATTGGGACTTCAAGTGACAAATTCT
Found at i:9742609 original size:8 final size:8
Alignment explanation
Indices: 9742593--9742630 Score: 53
Period size: 7 Copynumber: 4.9 Consensus size: 8
9742583 ATCTTTAAAC
9742593 TTTTT-AT
1 TTTTTAAT
9742600 TTTTTAAT
1 TTTTTAAT
9742608 TTTTT-AT
1 TTTTTAAT
9742615 TTTTTCAAT
1 TTTTT-AAT
9742624 TTTTTAA
1 TTTTTAA
9742631 CTAACACGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
7 12 0.43
8 9 0.32
9 7 0.25
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTAAT
Found at i:9742613 original size:15 final size:16
Alignment explanation
Indices: 9742593--9742629 Score: 67
Period size: 15 Copynumber: 2.4 Consensus size: 16
9742583 ATCTTTAAAC
9742593 TTTTTATTTTTT-AAT
1 TTTTTATTTTTTCAAT
9742608 TTTTTATTTTTTCAAT
1 TTTTTATTTTTTCAAT
9742624 TTTTTA
1 TTTTTA
9742630 ACTAACACGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 12 0.57
16 9 0.43
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTATTTTTTCAAT
Found at i:9744101 original size:17 final size:16
Alignment explanation
Indices: 9744079--9744151 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 16
9744069 TAATTAAGAG
9744079 CTAGTTTAATAATTGAA
1 CTAGTTTAATAA-TGAA
*
9744096 CTAGTTTGATGAATGAA
1 CTAGTTTAAT-AATGAA
9744113 CTAGTTTAATTAATGAA
1 CTAGTTTAA-TAATGAA
* *
9744130 CTAACTTTATTAAATGAA
1 CT-AGTTTAAT-AATGAA
9744148 CTAG
1 CTAG
9744152 ATGCTTGAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
17 31 0.66
18 16 0.34
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (16 bp):
CTAGTTTAATAATGAA
Found at i:9744145 original size:18 final size:18
Alignment explanation
Indices: 9744107--9744150 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
9744097 TAGTTTGATG
*
9744107 AATGAACT-AGTTTAATT
1 AATGAACTAACTTTAATT
9744124 AATGAACTAACTTT-ATT
1 AATGAACTAACTTTAATT
9744141 AAATGAACTA
1 -AATGAACTA
9744151 GATGCTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 11 0.46
18 13 0.54
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (18 bp):
AATGAACTAACTTTAATT
Found at i:9746369 original size:10 final size:9
Alignment explanation
Indices: 9746349--9746387 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
9746339 ATTTTGTTTC
9746349 TTTTC-TTT
1 TTTTCATTT
9746357 TTTTCAATTT
1 TTTTC-ATTT
9746367 TTTTCATTT
1 TTTTCATTT
9746376 TTTTCATTT
1 TTTTCATTT
9746385 TTT
1 TTT
9746388 ATTTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
8 5 0.17
9 16 0.55
10 8 0.28
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCATTT
Found at i:9753035 original size:15 final size:16
Alignment explanation
Indices: 9753007--9753038 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
9752997 TTTTTTGTCA
9753007 TAGTTACTAAAATTTG
1 TAGTTACTAAAATTTG
9753023 TAGTTAC-AAAATTTG
1 TAGTTACTAAAATTTG
9753038 T
1 T
9753039 CACTATATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (16 bp):
TAGTTACTAAAATTTG
Found at i:9754297 original size:55 final size:55
Alignment explanation
Indices: 9754227--9754454 Score: 325
Period size: 55 Copynumber: 4.2 Consensus size: 55
9754217 AATGGCATTA
*
9754227 TGTGTGC-AACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTACTGGCACTG
1 TGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTG
*
9754281 TGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTT
1 TGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTG
* * * * * *
9754336 TGTGTGCAAACCTAAGAAATTTATAATAAGTTTTTGAATTTTCATAATCGCAATG
1 TGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTG
* * *
9754391 TTTGTGCAAATCTAAGAAATTCATAATAAGTTTATGAACTTTT-GTATTGGTACTG
1 TGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAA-TTTTCGTATTGGCACTG
*
9754446 GGTGTGCAA
1 TGTGTGCAA
9754455 CGCATGTAAT
Statistics
Matches: 152, Mismatches: 20, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
54 7 0.05
55 141 0.93
56 4 0.03
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.38
Consensus pattern (55 bp):
TGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTG
Found at i:9757735 original size:23 final size:23
Alignment explanation
Indices: 9757717--9757777 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
9757707 CTCGTATAAA
9757717 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
9757740 TGAACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
9757763 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
9757778 TATAAGATTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:9758405 original size:64 final size:64
Alignment explanation
Indices: 9758295--9758417 Score: 169
Period size: 64 Copynumber: 1.9 Consensus size: 64
9758285 ATCCCTTGAC
*
9758295 GGGTGCATCGATGCACTATCTATGCATCGATACATAAATCCTATTCGATGTTTATATTTAAGGG
1 GGGTGCATCGATGCACTATCTATGCATCGATACACAAATCCTATTCGATGTTTATATTTAAGGG
* * * *
9758359 GGGTGCATCGATGCACTA-CTTGTGCATCGATACACAGAT-GTCATTCGATGTTTGTATTT
1 GGGTGCATCGATGCACTATC-TATGCATCGATACACAAATCCT-ATTCGATGTTTATATTT
9758418 TAAATTAGTG
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
63 2 0.04
64 50 0.96
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (64 bp):
GGGTGCATCGATGCACTATCTATGCATCGATACACAAATCCTATTCGATGTTTATATTTAAGGG
Found at i:9766640 original size:22 final size:21
Alignment explanation
Indices: 9766601--9766642 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9766591 TTCATGTCTT
*
9766601 TTTTTCGAACAGTTTTTTTTC
1 TTTTTCGAACAGTATTTTTTC
*
9766622 TTTTTCGAACTGCTATTTTTT
1 TTTTTCGAACAG-TATTTTTT
9766643 TTCAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.14, C:0.14, G:0.10, T:0.62
Consensus pattern (21 bp):
TTTTTCGAACAGTATTTTTTC
Found at i:9767530 original size:14 final size:13
Alignment explanation
Indices: 9767486--9767533 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
9767476 TTAATCGAAG
9767486 AAAAATAAATAAAA
1 AAAAATAAA-AAAA
* *
9767500 TAAAATAAAAGCAA
1 AAAAATAAAA-AAA
*
9767514 AAAAATAAAAAAT
1 AAAAATAAAAAAA
9767527 AAAAATA
1 AAAAATA
9767534 TAACGGAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 9 0.32
14 19 0.68
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAA
Found at i:9772436 original size:19 final size:20
Alignment explanation
Indices: 9772412--9772460 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
9772402 TATCCTTTCT
9772412 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
9772431 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
9772451 -TATTATTATT
1 TTATT-TTATT
9772461 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:9772982 original size:23 final size:23
Alignment explanation
Indices: 9772956--9773003 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
9772946 CTCATATAAA
9772956 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
*
9772979 TGCACCGAAGTGCCGCGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
9773002 TG
1 TG
9773004 AATTGTAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.29, T:0.19
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:9773813 original size:64 final size:63
Alignment explanation
Indices: 9773698--9773817 Score: 159
Period size: 64 Copynumber: 1.9 Consensus size: 63
9773688 CATAAATCAT
* * * * *
9773698 ATTCGATGTTTGTATTTAAGGGGGTGGATCGATGCACTACTTGTGCATCGATACACTGATGGC
1 ATTCGATGTTTGTATTTAAAGGAGTGCATCAATGCACTACATGTGCATCGATACACTGATGGC
** *
9773761 ATTCGATGTTTGTATTTTAAATTAGTGCATCAATGCACTTCATGTGCATCGATACAC
1 ATTCGATGTTTGTA-TTTAAAGGAGTGCATCAATGCACTACATGTGCATCGATACAC
9773818 CTTGAACAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
63 14 0.29
64 34 0.71
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (63 bp):
ATTCGATGTTTGTATTTAAAGGAGTGCATCAATGCACTACATGTGCATCGATACACTGATGGC
Found at i:9783822 original size:19 final size:21
Alignment explanation
Indices: 9783798--9783871 Score: 57
Period size: 20 Copynumber: 3.6 Consensus size: 21
9783788 TACAGAAATG
*
9783798 GTATCGATACTATA-AT-GGA
1 GTATCGATACTATAGATAGAA
* *
9783817 GTATCGGTACCATAGTATAGAA
1 GTATCGATACTATAG-ATAGAA
* *
9783839 GTATCGATACTAGGAGA-A-AC
1 GTATCGATACTA-TAGATAGAA
9783859 GTATCGATACTAT
1 GTATCGATACTAT
9783872 GGATCTAGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
19 12 0.28
20 13 0.30
21 3 0.07
22 13 0.30
23 2 0.05
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (21 bp):
GTATCGATACTATAGATAGAA
Found at i:9784368 original size:55 final size:55
Alignment explanation
Indices: 9784285--9784557 Score: 404
Period size: 55 Copynumber: 5.0 Consensus size: 55
9784275 ACCAAATGGA
* *
9784285 ACTATGTGTGC-AAGCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTAGC
1 ACTATGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGC
*
9784339 ACTATGTGTGTAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGC
1 ACTATGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGC
* * *
9784394 ACTGTGTGTGAAAACCTAAGAAATTCATAATAAGTTTATGAATTTTTGTATTGGC
1 ACTATGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGC
* * **
9784449 ATTATGTGTGCAAACCTAAGAAATTCATAATATGTTTATGAATTTTTTTATTGGC
1 ACTATGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGC
* ** * *
9784504 ACTGTGTGTGCAAATTTAAGAAATTTATAATAAGTTTATGAATTTCCGTATTGG
1 ACTATGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGG
9784558 TATTGGGTGT
Statistics
Matches: 198, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
54 10 0.05
55 188 0.95
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.40
Consensus pattern (55 bp):
ACTATGTGTGCAAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGC
Found at i:9786977 original size:17 final size:17
Alignment explanation
Indices: 9786957--9787038 Score: 69
Period size: 17 Copynumber: 4.8 Consensus size: 17
9786947 TAGTCTAATA
9786957 AATGAACTAGTTTGATG
1 AATGAACTAGTTTGATG
* *
9786974 AATGAACTAGTTTAATT
1 AATGAACTAGTTTGATG
* *
9786991 AATGAACTAACTTT-ATTC
1 AATGAACT-AGTTTGA-TG
*
9787009 AATGAACTAG-ATGCATG
1 AATGAACTAGTTTG-ATG
*
9787026 AATGAAGTAGTTT
1 AATGAACTAGTTT
9787039 ACTAAATGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
16 1 0.02
17 35 0.69
18 15 0.29
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (17 bp):
AATGAACTAGTTTGATG
Found at i:9788185 original size:18 final size:18
Alignment explanation
Indices: 9788157--9788199 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
9788147 ACAAGTTCAT
*
9788157 AAATAATTAAAG-AATAAA
1 AAATAAATAAAGCAA-AAA
*
9788175 ATATAAATAAAGCAAAAA
1 AAATAAATAAAGCAAAAA
9788193 AAATAAA
1 AAATAAA
9788200 ACTGTAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (18 bp):
AAATAAATAAAGCAAAAA
Found at i:9789109 original size:15 final size:15
Alignment explanation
Indices: 9789089--9789133 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
9789079 TATTTATTTA
9789089 TTACATTTTGATCAT
1 TTACATTTTGATCAT
* *
9789104 TTACATTATGGATTA-
1 TTACATT-TTGATCAT
9789119 TTACATTTTGATCAT
1 TTACATTTTGATCAT
9789134 CGAGACATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
14 5 0.21
15 14 0.58
16 5 0.21
ACGTcount: A:0.29, C:0.11, G:0.09, T:0.51
Consensus pattern (15 bp):
TTACATTTTGATCAT
Found at i:9792181 original size:16 final size:16
Alignment explanation
Indices: 9792160--9792196 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
9792150 ACCGTTGGCT
9792160 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
9792176 GAGGCGGCTGGAGGCA
1 GAGGCGGCTGGAGGCA
9792192 GAGGC
1 GAGGC
9792197 TAGGGTTAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.57, T:0.05
Consensus pattern (16 bp):
GAGGCGGCTGGAGGCA
Found at i:9792308 original size:3 final size:3
Alignment explanation
Indices: 9792302--9792379 Score: 93
Period size: 3 Copynumber: 26.0 Consensus size: 3
9792292 TATATATATT
* * *
9792302 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * *
9792350 TAA TTA TTA TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
9792380 ATAAATCAAT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (3 bp):
TAA
Found at i:9792813 original size:112 final size:112
Alignment explanation
Indices: 9792615--9792907 Score: 441
Period size: 112 Copynumber: 2.6 Consensus size: 112
9792605 GACAGAGTCA
* ** * * * *
9792615 AAAGGTTGAATAAGCTCTTCTTATTATGAACTTC--C-TCTTCTTCAGATGAGGTCTTCTTATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
*
9792677 TGAACTTTCTCTGGAAATTTTAATCCATCAAGTGATAGATTTGAGCG
66 TGAACTTTCTCTGGAAATTCTAATCCATCAAGTGATAGATTTGAGCG
*
9792724 AAAGGTTGAAGAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* *
9792789 TGAACTTTCTCTGGCAAA-TCTAATCCATCAAGTGATGGATTTGAGTG
66 TGAACTTTCTCTGG-AAATTCTAATCCATCAAGTGATAGATTTGAGCG
9792836 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
9792901 ATGAACT
65 ATGAACT
9792908 CTCCTTCTTC
Statistics
Matches: 168, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
109 30 0.18
111 1 0.01
112 104 0.62
113 33 0.20
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (112 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
TGAACTTTCTCTGGAAATTCTAATCCATCAAGTGATAGATTTGAGCG
Found at i:9792935 original size:38 final size:38
Alignment explanation
Indices: 9792848--9793510 Score: 520
Period size: 38 Copynumber: 17.5 Consensus size: 38
9792838 AGGTTGAACA
9792848 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G
1 AATTCTTCTCATTATGAA---C-TC-TCCTTCTTCAGATGATG
9792890 --TTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
1 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
9792926 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACT-
1 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGA-TG
9792964 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
1 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
*
9793002 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACG
1 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
*
9793040 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACG
1 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
* * * *
9793078 AGTTCTTCTCATTATGAACTCT--ATCTGGCA-ATG-TT
1 AATTCTTCTCATTATGAACTCTCCTTCT-TCAGATGATG
* * * **** *** * **
9793113 AATCCATC-AATTGATGAA-T-TTAAACAAAAGGTTGAACA
1 AATTCTTCTCATT-ATGAACTCTCCTTCTTCA-GATG-ATG
9793151 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G
1 AATTCTTCTCATTATGAA---C-TC-TCCTTCTTCAGATGATG
*
9793193 --TTCTTCTCATTATGAACTCTTCTTCTTCAGATGACT-
1 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGA-TG
*
9793229 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACG
1 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
* * ** *
9793267 AGTTCTTCTCATTATGAACTCT-ATAT-GGCA-ATG-TT
1 AATTCTTCTCATTATGAACTCTCCT-TCTTCAGATGATG
* * * **** *** * **
9793302 AATCCATC-AATTGATGAA-T-TTAAACAAAAGGTTGAACA
1 AATTCTTCTCATT-ATGAACTCTCCTTCTTCA-GATG-ATG
9793340 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G
1 AATTCTTCTCATTATGAA---C-TC-TCCTTCTTCAGATGATG
*
9793382 --TTCTTCTCATTATGAACTCTTCTTCTTCAGATGACT-
1 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGA-TG
9793418 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
1 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
9793456 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGA-G
1 AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
*
9793493 --TTTTTCTCATTATGAACT
1 AATTCTTCTCATTATGAACT
9793511 TTCTCTGGCA
Statistics
Matches: 509, Mismatches: 65, Indels: 101
0.75 0.10 0.15
Matches are distributed among these distances:
33 2 0.00
34 11 0.02
35 82 0.16
36 20 0.04
37 11 0.02
38 312 0.61
39 7 0.01
40 48 0.09
43 4 0.01
44 6 0.01
45 6 0.01
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (38 bp):
AATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATG
Found at i:9793085 original size:19 final size:19
Alignment explanation
Indices: 9792911--9793086 Score: 52
Period size: 19 Copynumber: 9.3 Consensus size: 19
9792901 ATGAACTCTC
*
9792911 CTTCTTCAGATGATGAATT
1 CTTCTTCAGATGACGAATT
* *
9792930 CTTC-TCATTATGA--ACTCT
1 CTTCTTCA-GATGACGAAT-T
*
9792948 CCTTCTTCAGATGACTAATT
1 -CTTCTTCAGATGACGAATT
* *
9792968 CTTC-TCATTATGA--ACTCT
1 CTTCTTCA-GATGACGAAT-T
*
9792986 CCTTCTTCAGATGATGAATT
1 -CTTCTTCAGATGACGAATT
* *
9793006 CTTC-TCATTATGA--ACTCT
1 CTTCTTCA-GATGACGAAT-T
9793024 CCTTCTTCAGATGACGAATT
1 -CTTCTTCAGATGACGAATT
* *
9793044 CTTC-TCATTATGA--ACTCT
1 CTTCTTCA-GATGACGAAT-T
*
9793062 CCTTCTTCAGATGACGAGTT
1 -CTTCTTCAGATGACGAATT
9793082 CTTCT
1 CTTCT
9793087 CATTATGAAC
Statistics
Matches: 117, Mismatches: 16, Indels: 48
0.65 0.09 0.27
Matches are distributed among these distances:
17 8 0.07
18 16 0.14
19 69 0.59
20 16 0.14
21 8 0.07
ACGTcount: A:0.23, C:0.25, G:0.11, T:0.41
Consensus pattern (19 bp):
CTTCTTCAGATGACGAATT
Found at i:9793107 original size:303 final size:303
Alignment explanation
Indices: 9792736--9793288 Score: 900
Period size: 303 Copynumber: 1.8 Consensus size: 303
9792726 AGGTTGAAGA
* *
9792736 AATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 AATTCTTCTCATTATGAACTTCTTC-TCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTATCT
* * ***
9792801 GGCAAAT-CTAATCCATCAAGTGATGGATTTGAGTGAAAGGTTGAACAAATTCTTCTCATTATGA
65 GGC-AATGCTAATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGA
9792865 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCCTTCTTCAGATGA-TGAAT
129 ACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCCTTCTTCAGATGACT-AAT
*
9792929 TCTTCTCATTATGAACTCTCCTTCTTCAGATGACTAATTCTTCTCATTATGAACTCTCCTTCTTC
193 TCTTCTCATTATGAACTCTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCTCCTTCTTC
9792994 AGATGATGAATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACG
258 AGATGATGAATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACG
*
9793040 AATTCTTCTCATTATGAAC-TC-TC-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAT
1 AATTCTTCTCATTATGAACTTCTTCTCCTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTAT
* *
9793102 CTGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
63 CTGGCAATGCTAATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATG
*
9793167 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTTCTTCAGATGACTAAT
128 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCCTTCTTCAGATGACTAAT
*
9793232 TCTTCTCATTATGAACTCTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
193 TCTTCTCATTATGAACTCTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCT
9793289 ATATGGCAAT
Statistics
Matches: 231, Mismatches: 13, Indels: 11
0.91 0.05 0.04
Matches are distributed among these distances:
300 10 0.04
302 5 0.02
303 196 0.85
304 20 0.09
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.41
Consensus pattern (303 bp):
AATTCTTCTCATTATGAACTTCTTCTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCTATCTG
GCAATGCTAATCCATCAAGTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTCCTTCTTCAGATGACTAATTCT
TCTCATTATGAACTCTCCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCTCCTTCTTCAGA
TGATGAATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACG
Found at i:9793217 original size:19 final size:19
Alignment explanation
Indices: 9793193--9793288 Score: 74
Period size: 19 Copynumber: 5.1 Consensus size: 19
9793183 TTCAGATGAG
9793193 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
* *
9793212 TTCTTCTTCA-GATG-ACTAA
1 TTCTTC-TCATTATGAACT-C
9793231 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
* * **
9793250 TCCTTCTTCA-GATG-ACGAG
1 TTCTTC-TCATTATGAAC-TC
9793269 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
9793288 T
1 T
9793289 ATATGGCAAT
Statistics
Matches: 57, Mismatches: 12, Indels: 16
0.67 0.14 0.19
Matches are distributed among these distances:
18 11 0.19
19 35 0.61
20 11 0.19
ACGTcount: A:0.22, C:0.25, G:0.09, T:0.44
Consensus pattern (19 bp):
TTCTTCTCATTATGAACTC
Found at i:9793235 original size:189 final size:189
Alignment explanation
Indices: 9792964--9793477 Score: 921
Period size: 189 Copynumber: 2.7 Consensus size: 189
9792954 TCAGATGACT
9792964 AATTCTTCTCATTATGAA---C-TC-TCCTTCTTCAGATGATGAATTCTTCTCATTATGAACTCT
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGA-G--TTCTTCTCATTATGAACTCT
* *
9793024 CCTTCTTCAGATGACGAATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACGAGTTCTTCTCA
63 TCTTCTTCAGATGACTAATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACGAGTTCTTCTCA
*
9793089 TTATGAACTCTATCTGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACA
128 TTATGAACTCTATATGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACA
9793151 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
9793216 TCTTCAGATGACTAATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACGAGTTCTTCTCATTA
66 TCTTCAGATGACTAATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACGAGTTCTTCTCATTA
9793281 TGAACTCTATATGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACA
131 TGAACTCTATATGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACA
9793340 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
* *
9793405 TCTTCAGATGACTAATTCTTCTCATTATGAACTCTCCTTCTTCAGATGATGAATTCTTCTCATTA
66 TCTTCAGATGACTAATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACGAGTTCTTCTCATTA
9793470 TGAACTCT
131 TGAACTCT
9793478 CCTTCTTCAG
Statistics
Matches: 317, Mismatches: 5, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
187 18 0.06
189 280 0.88
190 1 0.00
191 3 0.01
192 15 0.05
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.41
Consensus pattern (189 bp):
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
TCTTCAGATGACTAATTCTTCTCATTATGAACTCTCCTTCTTCAGATGACGAGTTCTTCTCATTA
TGAACTCTATATGGCAATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACA
Found at i:9793406 original size:19 final size:19
Alignment explanation
Indices: 9793382--9793483 Score: 79
Period size: 19 Copynumber: 5.4 Consensus size: 19
9793372 TTCAGATGAG
9793382 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
* *
9793401 TTCTTCTTCA-GATG-ACTAA
1 TTCTTC-TCATTATGAACT-C
9793420 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
* *
9793439 TCCTTCTTCAGATGATGAA---
1 TTCTTC-TC--ATTATGAACTC
9793458 TTCTTCTCATTATGAACTC
1 TTCTTCTCATTATGAACTC
*
9793477 TCCTTCT
1 TTCTTCT
9793484 TCAGATGAGT
Statistics
Matches: 64, Mismatches: 9, Indels: 20
0.69 0.10 0.22
Matches are distributed among these distances:
16 7 0.11
18 8 0.12
19 34 0.53
20 8 0.12
22 7 0.11
ACGTcount: A:0.22, C:0.25, G:0.08, T:0.45
Consensus pattern (19 bp):
TTCTTCTCATTATGAACTC
Found at i:9793445 original size:22 final size:22
Alignment explanation
Indices: 9793420--9793485 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 22
9793410 AGATGACTAA
9793420 TTCTTCTCATTATGAACTCTCC
1 TTCTTCTCATTATGAACTCTCC
** *
9793442 TTCTTCAGATGATGAA------
1 TTCTTCTCATTATGAACTCTCC
9793458 TTCTTCTCATTATGAACTCTCC
1 TTCTTCTCATTATGAACTCTCC
9793480 TTCTTC
1 TTCTTC
9793486 AGATGAGTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 12
0.64 0.12 0.24
Matches are distributed among these distances:
16 13 0.41
22 19 0.59
ACGTcount: A:0.20, C:0.27, G:0.08, T:0.45
Consensus pattern (22 bp):
TTCTTCTCATTATGAACTCTCC
Found at i:9793701 original size:336 final size:336
Alignment explanation
Indices: 9793229--9794000 Score: 895
Period size: 336 Copynumber: 2.3 Consensus size: 336
9793219 TCAGATGACT
* * *
9793229 AATTCTTCTCATTATGAAC-TC-TC--CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTA
1 AATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTC
* * * *
9793290 TATGGC-AATGTTAATCCATCAATTGATGAATTTAAACAAAAGGTTGAACAAATTCTTCTCATTA
63 TCTGGCAAAT-CTAATCCATCAAATGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTA
** * * *
9793354 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCTTCTTCAGATGACTA
127 TGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTC--CAACTGCAAAAGA-TA
* * * * ** *** **
9793419 ATTCTTCTCA-TTAT-GAACTCTCCTTCTTCA-GATG-ATGAATTCTTCTCATTATGAA-C-TC-
189 ATCCATC-AAGTGATAG-A-T-TCCAGCAAAAGGATGAACAAATTCTTCTCATTATGAATCTTCA
* **** *
9793477 TCCTTCTTCAGATGAGTTTTTCTCATTATGAACTTTCTCTGGCAAATCA-AATCCATCAAGTGAT
250 TCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGG-AAAACATAATCCATCAAGTGAT
* *
9793541 TGATTTGAGCGAAAGGTTGAACA
314 AGATTTGAGCAAAAGGTTGAACA
9793564 AATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
1 AATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * *
9793629 GGCAAATCTAATCCATCAAGTGATGGATTTGAGCGAAAGGTTGAACAAATTCTTCTCATTATGAA
66 GGCAAATCTAATCCATCAAATGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA
* * *
9793694 TTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATC
131 CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCAACTGCAAAAGATAATCCATC
** *
9793759 AAGTGATAGATTTGAGCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCATCCTTCTTC
196 AAGTGATAGATTCCAGCAAAAGGATGAACAAATTCTTCTCATTATGAA--TCTTCATCCTTCTTC
* *
9793824 ATATGAGTTCTTCTCATTATGAACTCGAACTGGAAAAGATAATCCATCAAGTGATAGATTTGAGC
259 AGATGAGTTCTTCTCATTATGAACTCGAACTGGAAAACATAATCCATCAAGTGATAGATTTGAGC
9793889 AAAAGGTTGAACA
324 AAAAGGTTGAACA
*
9793902 AATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * *
9793967 TGGAAAAGCTGATCCATCAAATGATGGATTTAAA
65 TGGCAAATCTAATCCATCAAATGATGGATTTAAA
9794001 TCTTTGCTAA
Statistics
Matches: 372, Mismatches: 49, Indels: 28
0.83 0.11 0.06
Matches are distributed among these distances:
331 3 0.01
332 5 0.01
333 30 0.08
334 7 0.02
335 19 0.05
336 124 0.33
337 11 0.03
338 100 0.27
339 73 0.20
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (336 bp):
AATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
GGCAAATCTAATCCATCAAATGATGGATTTAAACAAAAGGTTGAACAAATTCTTCTCATTATGAA
CTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCCAACTGCAAAAGATAATCCATC
AAGTGATAGATTCCAGCAAAAGGATGAACAAATTCTTCTCATTATGAATCTTCATCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTCGAACTGGAAAACATAATCCATCAAGTGATAGATTTGAGCAA
AAGGTTGAACA
Found at i:9793771 original size:113 final size:113
Alignment explanation
Indices: 9793229--9793997 Score: 834
Period size: 113 Copynumber: 6.8 Consensus size: 113
9793219 TCAGATGACT
*
9793229 AATTCTTCTCATTATGAA---C-TC-TCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCT
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTT
* * * * * * * *
9793289 ATATGGCAATGTTAATCCATCAATTGAT-GAATTTAAACAAAAGGTTGAACA
63 CTCTGGAAAAGATAATCCATCAAGTGATAG-ATTTGAGCAAAAGGTTGAACA
9793340 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTTCT
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTC-
** * * * * * * **** *** * **
9793405 TCTTCAGATGACTAATTCTTCTCA-TTAT-GAACTCTCCTTCTTCA-GATG-ATG
64 TCTGGAAAAGA-TAATCCATC-AAGTGATAG-A-T-TTGAGCAAAAGGTTGAACA
*
9793456 AATTCTTCTCATTATGAA---C-TC-TCCTTCTTCAGATGAGTTTTTCTCATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
** * *
9793516 TGGCAAATCA-AATCCATCAAGTGATTGATTTGAGCGAAAGGTTGAACA
66 TGG-AAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
9793564 AATTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* ** * *
9793628 TGGCAAATCTAATCCATCAAGTGATGGATTTGAGCGAAAGGTTGAACA
66 TGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
* ****
9793676 AATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAAC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
9793741 TGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
66 TGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
* * ****
9793789 AATTCTTCTCATTATGAACTTCTTCATCCTTCTTCATATGAGTTCTTCTCATTATGAACTCGAAC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
9793854 TGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
66 TGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
*
9793902 AATTCTTCTCATTATGAACTTATTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
1 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
* * * *
9793967 TGGAAAAGCTGATCCATCAAATGATGGATTT
66 TGGAAAAGATAATCCATCAAGTGATAGATTT
9793998 AAATCTTTGC
Statistics
Matches: 564, Mismatches: 71, Indels: 44
0.83 0.10 0.06
Matches are distributed among these distances:
106 3 0.01
107 5 0.01
108 29 0.05
109 4 0.01
110 7 0.01
111 54 0.10
112 106 0.19
113 294 0.52
114 2 0.00
115 7 0.01
116 45 0.08
117 5 0.01
118 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (113 bp):
AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTC
TGGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACA
Found at i:9794424 original size:22 final size:22
Alignment explanation
Indices: 9794399--9794459 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
9794389 TCTGATAAAG
9794399 CTTTCATCTTTGAAAAGAGAAT
1 CTTTCATCTTTGAAAAGAGAAT
* *
9794421 CTTTCATCTTTAAAAAGGGAAT
1 CTTTCATCTTTGAAAAGAGAAT
* *
9794443 CTATCATCTATGAAAAG
1 CTTTCATCTTTGAAAAG
9794460 TGTAGATGTA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (22 bp):
CTTTCATCTTTGAAAAGAGAAT
Found at i:9799290 original size:10 final size:10
Alignment explanation
Indices: 9799277--9799303 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9799267 CAATTTTCCC
9799277 CTTTTTTTTT
1 CTTTTTTTTT
9799287 CTTTTTTTTT
1 CTTTTTTTTT
9799297 CTTTTTT
1 CTTTTTT
9799304 CTTTTCTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:9799316 original size:12 final size:11
Alignment explanation
Indices: 9799277--9799319 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
9799267 CAATTTTCCC
9799277 CTTTTT-TTTT
1 CTTTTTCTTTT
9799287 CTTTTT-TTTT
1 CTTTTTCTTTT
9799297 CTTTTTTCTTTT
1 C-TTTTTCTTTT
9799309 CTTCTTTCTTT
1 CTT-TTTCTTT
9799320 GCTGGATGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 11 0.37
11 7 0.23
12 12 0.40
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
CTTTTTCTTTT
Found at i:9813982 original size:21 final size:20
Alignment explanation
Indices: 9813935--9813984 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
9813925 TAATATTATG
*
9813935 TAATA-TATCAAATATAATA
1 TAATATTATAAAATATAATA
* *
9813954 TAAAATTATAAAATATATTCA
1 TAATATTATAAAATATAAT-A
9813975 TAATATTATA
1 TAATATTATA
9813985 TTTTAGAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
19 4 0.16
20 11 0.44
21 10 0.40
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATATTATAAAATATAATA
Found at i:9815783 original size:18 final size:18
Alignment explanation
Indices: 9815760--9815799 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9815750 ATTTTTATCA
9815760 TTTAATAAAAAAAATAAC
1 TTTAATAAAAAAAATAAC
* * *
9815778 TTTAATTAAAACAATAAT
1 TTTAATAAAAAAAATAAC
9815796 TTTA
1 TTTA
9815800 CAGTATGCAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTAATAAAAAAAATAAC
Found at i:9817416 original size:23 final size:22
Alignment explanation
Indices: 9817394--9817435 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9817384 GGTTTTCCCT
*
9817394 TTTCTTTCTGAATCCTCCCCCC
1 TTTCTTTCTGAATCATCCCCCC
*
9817416 TTTGTTTCTGAATCATCCCC
1 TTTCTTTCTGAATCATCCCC
9817436 TGATCTACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.38, G:0.07, T:0.43
Consensus pattern (22 bp):
TTTCTTTCTGAATCATCCCCCC
Found at i:9818361 original size:132 final size:132
Alignment explanation
Indices: 9818083--9818750 Score: 567
Period size: 132 Copynumber: 5.1 Consensus size: 132
9818073 AGATATTTTT
* * * ** * * *
9818083 GAAGATC-AATATGAAAAAGAGATCTGCTCCG-TTGTTCTTCAGGGTAGATCAGATATG-GAAAC
1 GAAGATCAAATCTGAAAAAGGGATCCGCTCCGCTACTTATTCAGGGTAGATCAGATCTGAAAAAC
* * ** * * * *
9818145 TTTGATTCACTTTACTGCTTTTCAAAGAAGATTTAATCGAGGTTGATTTGC-TCATTGTTCTTC-
66 TTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTTGATTTACTTCACTGCTCTTCA
9818208 AG
131 AG
* ** * * * *
9818210 GAAAGATCAAATATGGAAAAAAGGGATCCGCTTTGATACGT-TCCAGGGTATATCAGATCTGAAA
1 G-AAGATCAAATCT-G-AAAAAGGGATCCGCTCCGCTACTTATTCAGGGTAGATCAGATCTGAAA
* * * * *
9818274 AAGTTTGATTCATTTCACTGCTCTTTAGGGAAGATTGAATTGGGGTTGATTTACTTCACTGCTCT
63 AACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTTGATTTACTTCACTGCTCT
9818339 TCAAG
128 TCAAG
** * * * * *
9818344 GAAGATCAAATCTGAAAAAGGGATATGTTCCGCTAC-TCTTCAGAGTAGGTCAGATCT-AGAAAC
1 GAAGATCAAATCTGAAAAAGGGATCCGCTCCGCTACTTATTCAGGGTAGATCAGATCTGAAAAAC
* * * * ** *
9818407 GTTGAATT-AATTCACTACTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTTCACTGCTCTTT
66 TTTG-ATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTTGATTTACTTCACTGCTCTTC
*
9818471 AGG
130 AAG
* *
9818474 GAAGATCAAATCTGAAAATAATGGA-CCAGCTCCGCTA-TTATTCAGGGTAGATCAGATCT-AGA
1 GAAGATCAAATCTG-AAA-AAGGGATCC-GCTCCGCTACTTATTCAGGGTAGATCAGATCTGAAA
* * * * *
9818536 AACTTTGATTCACTTCACTTCTCTTCAGGGAAGATTAAATCAAGGTTGATTTGA-TTCAATTCTC
63 AACTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTTGATTT-ACTTCACTGCTC
9818600 TTCAGAG
127 TTCA-AG
* * *** * *
9818607 AAAGATCAAATACTGAAAAAGAGATCTTATCCGCTGCTT-TTCAGGGTAGATCAGATCT-AGAAA
1 GAAGATCAAAT-CTGAAAAAGGGATCCGCTCCGCTACTTATTCAGGGTAGATCAGATCTGAAAAA
* * * * *
9818670 CATTGATTCACTTCACTGCTCTTCAGGGAAGATTCAATCGAGTTTGATTT-GTTCACTACTCTTC
65 CTTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTTGATTTACTTCACTGCTCTTC
*
9818734 AGG
130 AAG
9818737 GAAGATCAAATCTG
1 GAAGATCAAATCTG
9818751 TATATCAAAA
Statistics
Matches: 438, Mismatches: 82, Indels: 40
0.78 0.15 0.07
Matches are distributed among these distances:
127 1 0.00
128 6 0.01
129 8 0.02
130 83 0.19
131 83 0.19
132 213 0.49
133 38 0.09
134 6 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (132 bp):
GAAGATCAAATCTGAAAAAGGGATCCGCTCCGCTACTTATTCAGGGTAGATCAGATCTGAAAAAC
TTTGATTCACTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTTGATTTACTTCACTGCTCTTCA
AG
Found at i:9821894 original size:23 final size:23
Alignment explanation
Indices: 9821868--9821950 Score: 139
Period size: 23 Copynumber: 3.6 Consensus size: 23
9821858 CATTTTATAT
**
9821868 GGCACTTAAGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
9821891 GGCACTTCGGTGCAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
9821914 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
9821937 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
9821951 TTTATATGAG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 57 1.00
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:9822895 original size:14 final size:14
Alignment explanation
Indices: 9822876--9822911 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
9822866 TGTCTTGCTG
9822876 ATAGAATAAGTTTA
1 ATAGAATAAGTTTA
9822890 ATAGAATAAGTTTA
1 ATAGAATAAGTTTA
9822904 ATAGAATA
1 ATAGAATA
9822912 CAATTGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (14 bp):
ATAGAATAAGTTTA
Found at i:9825812 original size:20 final size:23
Alignment explanation
Indices: 9825748--9825812 Score: 64
Period size: 24 Copynumber: 2.9 Consensus size: 23
9825738 CATATATGGA
*
9825748 TAAGGAGTGCATCGATGCACATGT
1 TAAGGAATGCATCGATGCAC-TGT
* * *
9825772 TAAGGGATGCATCGGTACACTG-
1 TAAGGAATGCATCGATGCACTGT
9825794 T-A-GAATGCATCGATGCACT
1 TAAGGAATGCATCGATGCACT
9825813 TCAAGGGGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 14 0.41
21 1 0.03
22 1 0.03
23 2 0.06
24 16 0.47
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (23 bp):
TAAGGAATGCATCGATGCACTGT
Found at i:9827212 original size:23 final size:23
Alignment explanation
Indices: 9827144--9827204 Score: 113
Period size: 23 Copynumber: 2.7 Consensus size: 23
9827134 ACATTTTATA
9827144 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
*
9827167 CGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
9827190 TGGCACTTCGGTGCA
1 TGGCACTTCGGTGCA
9827205 TTTATACGAG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:9828612 original size:45 final size:45
Alignment explanation
Indices: 9828163--9828615 Score: 521
Period size: 45 Copynumber: 10.1 Consensus size: 45
9828153 TCTTCTTTGT
* * * * * **
9828163 AGTCAAGAAAGACATCACTAAAAGGTTGAGTCCTCTTAATAAGAA
1 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
* * *
9828208 A-ACTAAGAAGGACAACACTAAAAGATTAACTCCTCTTCACGAGAA
1 AGTC-AAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
* * *
9828253 AGTCAAGAAGGACAACAATAAAAGATTGATTCCTCTTCACGAGAA
1 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
* * * * * *
9828298 AGTAAAAAATGACAACACTGAAAGACTGACTCATCTTCACGAGAG
1 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
*
9828343 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACAAGAA
1 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
* * * * * *
9828388 AGCCAAGAAGGACAACATTAAAATATTGGCTCTTCTTCACGAGAA
1 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
* * * *
9828433 AGTCAAGAAGGACGACACTAAAAGAATGACTCTTCTTCACGAGAA
1 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
*
9828478 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTACACGAGAA
1 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
* * * *
9828523 AGTCAAGAATGAGAATACCAAAAGATTGACTCTTCTTCACGAGAA
1 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
* * * * * *
9828568 AGCCAAGAATGACATCACTAAAAGATTAACTCTTCTTTATGAGAA
1 AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
9828613 AGT
1 AGT
9828616 AAAGTTGAAG
Statistics
Matches: 345, Mismatches: 61, Indels: 4
0.84 0.15 0.01
Matches are distributed among these distances:
44 1 0.00
45 343 0.99
46 1 0.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (45 bp):
AGTCAAGAATGACAACACTAAAAGATTGACTCCTCTTCACGAGAA
Found at i:9828719 original size:37 final size:37
Alignment explanation
Indices: 9828657--9828728 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
9828647 GAAGGACAAA
* *
9828657 AACAAATTATTAGAGAAACGATCCTATGAAAGACTTT
1 AACAAATTATTAGAGAAACCATCCTAAGAAAGACTTT
* *
9828694 AACAAATT-TCTAGAGAAACCCTCCTAAGAAGGACT
1 AACAAATTAT-TAGAGAAACCATCCTAAGAAAGACT
9828729 AGAGTGAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 1 0.03
37 29 0.97
ACGTcount: A:0.44, C:0.18, G:0.14, T:0.24
Consensus pattern (37 bp):
AACAAATTATTAGAGAAACCATCCTAAGAAAGACTTT
Found at i:9830064 original size:3 final size:3
Alignment explanation
Indices: 9830056--9830090 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
9830046 TTTATTTTCT
* *
9830056 TTC TTC TTC TTC TTC TTC TTC TTC ATC TTC CTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
9830091 TTTTTTCTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:9830134 original size:14 final size:14
Alignment explanation
Indices: 9830115--9830157 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
9830105 TTTTTCTTCC
9830115 ATTTTTCTTTTCTT
1 ATTTTTCTTTTCTT
*
9830129 ATTTTTCATTTCTT
1 ATTTTTCTTTTCTT
* *
9830143 TTTTATTTTTTTCTT
1 ATTT-TTCTTTTCTT
9830158 TCTTTTTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 16 0.67
15 8 0.33
ACGTcount: A:0.09, C:0.12, G:0.00, T:0.79
Consensus pattern (14 bp):
ATTTTTCTTTTCTT
Found at i:9830153 original size:19 final size:18
Alignment explanation
Indices: 9830118--9830165 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
9830108 TTCTTCCATT
9830118 TTTCTTTTCTTA-TTTTTC
1 TTTCTTTT-TTATTTTTTC
9830136 ATTTCTTTTTTATTTTTTTC
1 -TTTCTTTTTTA-TTTTTTC
9830156 TTTCTTTTTT
1 TTTCTTTTTT
9830166 CTATCTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.11
19 18 0.67
20 6 0.22
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTCTTTTTTATTTTTTC
Found at i:9830153 original size:33 final size:34
Alignment explanation
Indices: 9830116--9830194 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
9830106 TTTTCTTCCA
9830116 TTTTTCTTTTCTTATTTTTC-AT-TTCTTTTTTAT-
1 TTTTT-TTTTCTT-TTTTTCTATCTTCTTTTTTATC
*
9830149 TTTTTTCTTTC-TTTTTTCTATCTTTTTTTTTATC
1 TTTTTT-TTTCTTTTTTTCTATCTTCTTTTTTATC
9830183 TTTTTTTTTCTT
1 TTTTTTTTTCTT
9830195 GAATATGAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
31 6 0.15
32 4 0.10
33 23 0.57
34 7 0.17
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (34 bp):
TTTTTTTTTCTTTTTTTCTATCTTCTTTTTTATC
Found at i:9830157 original size:15 final size:15
Alignment explanation
Indices: 9830116--9830176 Score: 52
Period size: 15 Copynumber: 3.8 Consensus size: 15
9830106 TTTTCTTCCA
9830116 TTTTTCTTTTCTTATTT
1 TTTTTCTTTT-TTA-TT
9830133 TTCATTTCTTTTTTATT
1 TT--TTTCTTTTTTATT
9830150 TTTTTCTTTCTTT-TT
1 TTTTTCTTT-TTTATT
* *
9830165 TCTATCTTTTTT
1 TTTTTCTTTTTT
9830177 TTTATCTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
14 3 0.08
15 16 0.41
16 3 0.08
17 6 0.15
18 3 0.08
19 8 0.21
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCTTTTTTATT
Found at i:9830190 original size:12 final size:12
Alignment explanation
Indices: 9830141--9830191 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
9830131 TTTTCATTTC
9830141 TTTTTTAT-TTT
1 TTTTTTATCTTT
*
9830152 TTTCTT-TC-TT
1 TTTTTTATCTTT
*
9830162 TTTTCTATCTTT
1 TTTTTTATCTTT
9830174 TTTTTTATCTTT
1 TTTTTTATCTTT
9830186 TTTTTT
1 TTTTTT
9830192 CTTGAATATG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 7 0.21
11 7 0.21
12 19 0.58
ACGTcount: A:0.06, C:0.10, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTATCTTT
Found at i:9833174 original size:15 final size:16
Alignment explanation
Indices: 9833147--9833176 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
9833137 TTTTGTTTTT
9833147 AATTATATATTATATA
1 AATTATATATTATATA
9833163 AATTAT-TATTATAT
1 AATTATATATTATAT
9833177 TAATATTACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTATATATTATATA
Found at i:9840829 original size:25 final size:26
Alignment explanation
Indices: 9840786--9840834 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
9840776 GGGTATGCTA
*
9840786 AAGGCCCATTTCCAGTCAGAAATATG
1 AAGGCCCATTTCCAATCAGAAATATG
*
9840812 AAGGCTCA-TTCCAATCAGAAATA
1 AAGGCCCATTTCCAATCAGAAATA
9840835 GAACGCTGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.22
Consensus pattern (26 bp):
AAGGCCCATTTCCAATCAGAAATATG
Found at i:9842401 original size:119 final size:119
Alignment explanation
Indices: 9842188--9842540 Score: 573
Period size: 119 Copynumber: 3.0 Consensus size: 119
9842178 AGTTGTTTAA
* *
9842188 AAAATGAGAAAGTGATTTTCAAAGTTTTTCATTTAATGTTCTAGAAAATTAAATCCTTC-GGGTA
1 AAAATGAGAAAGAGATTTTCAAAGTTTTTCATTTAATTTTCTAGAAAATTAAATCC-TCAGGGTA
* *
9842252 ATTTGTAAAGCCTCCGGGTCATCTGTAAAACTTCAGGGTATGATATTTTCGCATG
65 ATTTGTAAAGCCTCCGGGTCATCTGTAAAACTTCAGGGTAGGATATTTTCACATG
*
9842307 AAAATGAGAAAGAGATTTTCAAAGTTTTTTATTTAATTTTCTAGAAAATTAAATCCTCAGGGTAA
1 AAAATGAGAAAGAGATTTTCAAAGTTTTTCATTTAATTTTCTAGAAAATTAAATCCTCAGGGTAA
*
9842372 TTTGTAAAGCCTCCGGGTCATCTGCAAAACTTCAGGGTAGGATATTTTCACATG
66 TTTGTAAAGCCTCCGGGTCATCTGTAAAACTTCAGGGTAGGATATTTTCACATG
* *
9842426 AAAATGAGAAAGAGATTTTCAAAGTTTCTCATTTAATTTTTTAGAAAATTAAATCCTCAGGGTAA
1 AAAATGAGAAAGAGATTTTCAAAGTTTTTCATTTAATTTTCTAGAAAATTAAATCCTCAGGGTAA
* * * * *
9842491 TTTGTAAAGCCTCTGGGTCATTTGTAAAACCTCTGGGTAGGATGTTTTCA
66 TTTGTAAAGCCTCCGGGTCATCTGTAAAACTTCAGGGTAGGATATTTTCA
9842541 TTGTTGATTT
Statistics
Matches: 218, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
118 2 0.01
119 216 0.99
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (119 bp):
AAAATGAGAAAGAGATTTTCAAAGTTTTTCATTTAATTTTCTAGAAAATTAAATCCTCAGGGTAA
TTTGTAAAGCCTCCGGGTCATCTGTAAAACTTCAGGGTAGGATATTTTCACATG
Found at i:9842503 original size:20 final size:20
Alignment explanation
Indices: 9842475--9842529 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
9842465 TTTAGAAAAT
* *
9842475 TAAATCCTCAGGGTAATTTG
1 TAAAACCTCTGGGTAATTTG
* *
9842495 TAAAGCCTCTGGGTCATTTG
1 TAAAACCTCTGGGTAATTTG
9842515 TAAAACCTCTGGGTA
1 TAAAACCTCTGGGTA
9842530 GGATGTTTTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.33
Consensus pattern (20 bp):
TAAAACCTCTGGGTAATTTG
Found at i:9842695 original size:11 final size:11
Alignment explanation
Indices: 9842666--9842700 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
9842656 TTCGTTTTTA
9842666 ATTATATATTAT
1 ATTAT-TATTAT
9842678 ATATATTATTAT
1 AT-TATTATTAT
9842690 ATTATTATTAT
1 ATTATTATTAT
9842701 TGCTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.41
12 10 0.45
13 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:9844051 original size:6 final size:6
Alignment explanation
Indices: 9844009--9844066 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
9843999 TTTTACTATT
* *
9844009 TTAT-A TTATAA TTATTAA TTATTA TTATAA GTT-TAA TTATAA -TATTA
1 TTATAA TTATAA TTA-TAA TTATAA TTATAA -TTATAA TTATAA TTATAA
*
9844056 GTATAA TTATA
1 TTATAA TTATA
9844067 TATATTAGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
5 10 0.23
6 25 0.58
7 8 0.19
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (6 bp):
TTATAA
Found at i:9844073 original size:18 final size:18
Alignment explanation
Indices: 9844024--9844087 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
9844014 TTATAATTAT
* *
9844024 TAATTAT-TATTATAAGTT
1 TAATTATATA-TATTAGTA
9844042 TAATTATA-ATATTAGTA
1 TAATTATATATATTAGTA
*
9844059 TAATTATATATATTAGGA
1 TAATTATATATATTAGTA
*
9844077 TAATTTTATAT
1 TAATTATATAT
9844088 TTTAATAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
17 14 0.35
18 26 0.65
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (18 bp):
TAATTATATATATTAGTA
Found at i:9846710 original size:12 final size:12
Alignment explanation
Indices: 9846693--9846717 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9846683 AATTTGGACC
9846693 TGTTGTTAGGCT
1 TGTTGTTAGGCT
9846705 TGTTGTTAGGCT
1 TGTTGTTAGGCT
9846717 T
1 T
9846718 CTCTTGGTTG
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:0.08, C:0.08, G:0.32, T:0.52
Consensus pattern (12 bp):
TGTTGTTAGGCT
Found at i:9848090 original size:2 final size:2
Alignment explanation
Indices: 9848085--9848146 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
9848075 TGGCACACAA
9848085 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9848127 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
9848147 GGAGAGAGGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9852286 original size:2 final size:2
Alignment explanation
Indices: 9852279--9852309 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9852269 TTGATCCTTG
9852279 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9852310 GGGTAAACTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9853358 original size:6 final size:7
Alignment explanation
Indices: 9853342--9853371 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
9853332 TATAAATACC
9853342 TTTTAAT
1 TTTTAAT
9853349 TTTTAAT
1 TTTTAAT
9853356 TTTTAAT
1 TTTTAAT
9853363 TTTT-AT
1 TTTTAAT
9853369 TTT
1 TTT
9853372 CATTCATTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTAAT
Found at i:9855286 original size:21 final size:20
Alignment explanation
Indices: 9855262--9855301 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9855252 TGTTGTATTA
*
9855262 TGTTGGAAATTAATGTTAGAT
1 TGTT-GAAACTAATGTTAGAT
*
9855283 TGTTGAAACTGATGTTAGA
1 TGTTGAAACTAATGTTAGA
9855302 ATGTGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.40
Consensus pattern (20 bp):
TGTTGAAACTAATGTTAGAT
Found at i:9855546 original size:43 final size:43
Alignment explanation
Indices: 9855498--9855612 Score: 133
Period size: 43 Copynumber: 2.7 Consensus size: 43
9855488 TTAGCATCGA
* *
9855498 AAGATTTTTAGGAATTTAATTTCTAATGTATGCCTATATCATT
1 AAGATTTTTAGCAATTTAATTTCTAATGTATGCCTATATCAGT
* * * * *
9855541 AAGA-TTCTAACATATTTAATTTCTAATGTTTGCCTATGTTAGT
1 AAGATTTTTAGCA-ATTTAATTTCTAATGTATGCCTATATCAGT
* *
9855584 AAGGTTTTTAGTAATTTAATTTCTAATGT
1 AAGATTTTTAGCAATTTAATTTCTAATGT
9855613 TTTCCTATTT
Statistics
Matches: 59, Mismatches: 11, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
42 5 0.08
43 49 0.83
44 5 0.08
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.48
Consensus pattern (43 bp):
AAGATTTTTAGCAATTTAATTTCTAATGTATGCCTATATCAGT
Found at i:9856257 original size:21 final size:20
Alignment explanation
Indices: 9856233--9856272 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
9856223 TGTTGTATTA
*
9856233 TGTTGGAAATTAATGTTAGAT
1 TGTT-GAAACTAATGTTAGAT
*
9856254 TGTTGAAACTGATGTTAGA
1 TGTTGAAACTAATGTTAGA
9856273 ATGTGAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.03, G:0.25, T:0.40
Consensus pattern (20 bp):
TGTTGAAACTAATGTTAGAT
Found at i:9856271 original size:971 final size:971
Alignment explanation
Indices: 9854663--9856603 Score: 3801
Period size: 971 Copynumber: 2.0 Consensus size: 971
9854653 AAATTTTGTT
9854663 TTTCATTTTTTAGCAATTTCTTTTGGATTTTGGATCAAACCATGAAATAGAAAATTGTTCTATTC
1 TTTCATTTTTTAGCAATTTCTTTTGGATTTTGGATCAAACCATGAAATAGAAAATTGTTCTATTC
*
9854728 GAAGAGTTCTTTCATTTGGTACCATTATTGCATGCTAATCTTGCTTGAGTGCTAAGATCCCAAAT
66 GAAGAGCTCTTTCATTTGGTACCATTATTGCATGCTAATCTTGCTTGAGTGCTAAGATCCCAAAT
9854793 TTTAGGGTTTATGTTCATGTTAGGGTTTTATGAATTGATGATGGATTTTGAGGTTATTGAGGTTG
131 TTTAGGGTTTATGTTCATGTTAGGGTTTTATGAATTGATGATGGATTTTGAGGTTATTGAGGTTG
9854858 TAGAATCATTTACAAGATTGTTTGATGATCAAAACCACCTAAAAAGATTATTATGATTTTTGGCC
196 TAGAATCATTTACAAGATTGTTTGATGATCAAAACCACCTAAAAAGATTATTATGATTTTTGGCC
9854923 TAAACCCTAAATTAAGGGAAGTTTATGATTTGATGAAATTGAGTTAGGGTTTGATTGTATAGTTT
261 TAAACCCTAAATTAAGGGAAGTTTATGATTTGATGAAATTGAGTTAGGGTTTGATTGTATAGTTT
9854988 TAAAATATTGCATAGAGGGTGATTTAATGCTAGAATCAATTGAAATCAAGTGAAAATCATGGAAC
326 TAAAATATTGCATAGAGGGTGATTTAATGCTAGAATCAATTGAAATCAAGTGAAAATCATGGAAC
*
9855053 CCTAATCTTTAGACTTTCGGATATGGTTTTAAAAGGTGAGAAAAAATATGGAAATATTATGTAAG
391 CCTAATCTTTAGACTTTCAGATATGGTTTTAAAAGGTGAGAAAAAATATGGAAATATTATGTAAG
9855118 GGTTGGAAATGATGTAGGAATGATTATACAAGCTTTGAAACATTGTTTGGTTCAATTTGTAATAT
456 GGTTGGAAATGATGTAGGAATGATTATACAAGCTTTGAAACATTGTTTGGTTCAATTTGTAATAT
9855183 TGTGAAAGTTGGTGGACCTATTTAGTAATTATGGAAAATTATGAGATCAATATGTAATTGTTTAA
521 TGTGAAAGTTGGTGGACCTATTTAGTAATTATGGAAAATTATGAGATCAATATGTAATTGTTTAA
9855248 TAGTTGTTGTATTATGTTGGAAATTAATGTTAGATTGTTGAAACTGATGTTAGAATGTGAAATTG
586 TAGTTGTTGTATTATGTTGGAAATTAATGTTAGATTGTTGAAACTGATGTTAGAATGTGAAATTG
*
9855313 GATTATTTTGGAAAGTTGGTCAAAGTTGTGGTTCAAATCACAAATATGGAAAAGTTGGGAACTTA
651 GATTATTTTGGAAAATTGGTCAAAGTTGTGGTTCAAATCACAAATATGGAAAAGTTGGGAACTTA
9855378 AGTGAAAATATTATGTGAATTTTGGATAAATATGAATAAAAAGGAACTTAAATGGTCAATTTGAA
716 AGTGAAAATATTATGTGAATTTTGGATAAATATGAATAAAAAGGAACTTAAATGGTCAATTTGAA
* *
9855443 GTGTTAAGGTCAACATTTATGTTGTGACTTGAAATTTGTATCGAATTAGCATCGAAAGATTTTTA
781 GTGTTAAGGTCAACATTTATGTTGTGACATGAAATTTGTATCGAATGAGCATCGAAAGATTTTTA
9855508 GGAATTTAATTTCTAATGTATGCCTATATCATTAAGATTCTAACATATTTAATTTCTAATGTTTG
846 GGAATTTAATTTCTAATGTATGCCTATATCATTAAGATTCTAACATATTTAATTTCTAATGTTTG
*
9855573 CCTATGTTAGTAAGGTTTTTAGTAATTTAATTTCTAATGTTTTCCTATTTTTAATTTGTAC
911 CCTATGTTAGTAAGGTTTTTAGTAATTTAATTTCTAATGTTTGCCTATTTTTAATTTGTAC
9855634 TTTCATTTTTTAGCAATTTCTTTTGGATTTTGGATCAAACCATGAAATAGAAAATTGTTCTATTC
1 TTTCATTTTTTAGCAATTTCTTTTGGATTTTGGATCAAACCATGAAATAGAAAATTGTTCTATTC
*
9855699 GAAGAGCTCTTTCATTTGGTACTATTATTGCATGCTAATCTTGCTTGAGTGCTAAGATCCCAAAT
66 GAAGAGCTCTTTCATTTGGTACCATTATTGCATGCTAATCTTGCTTGAGTGCTAAGATCCCAAAT
9855764 TTTAGGGTTTATGTTCATGTTAGGGTTTTATGAATTGATGATGGATTTTGAGGTTATTGAGGTTG
131 TTTAGGGTTTATGTTCATGTTAGGGTTTTATGAATTGATGATGGATTTTGAGGTTATTGAGGTTG
*
9855829 TAGAATCATTTACAAGATTGTTTGATGATCAAAACCACCTAAAAAGGTTATTATGATTTTTGGCC
196 TAGAATCATTTACAAGATTGTTTGATGATCAAAACCACCTAAAAAGATTATTATGATTTTTGGCC
9855894 TAAACCCTAAATTAAGGGAAGTTTATGATTTGATGAAATTGAGTTAGGGTTTGATTGTATAGTTT
261 TAAACCCTAAATTAAGGGAAGTTTATGATTTGATGAAATTGAGTTAGGGTTTGATTGTATAGTTT
9855959 TAAAATATTGCATAGAGGGTGATTTAATGCTAGAATCAATTGAAATCAAGTGAAAATCATGGAAC
326 TAAAATATTGCATAGAGGGTGATTTAATGCTAGAATCAATTGAAATCAAGTGAAAATCATGGAAC
9856024 CCTAATCTTTAGACTTTCAGATATGGTTTTAAAAGGTGAGAAAAAATATGGAAATATTATGTAAG
391 CCTAATCTTTAGACTTTCAGATATGGTTTTAAAAGGTGAGAAAAAATATGGAAATATTATGTAAG
9856089 GGTTGGAAATGATGTAGGAATGATTATACAAGCTTTGAAACATTGTTTGGTTCAATTTGTAATAT
456 GGTTGGAAATGATGTAGGAATGATTATACAAGCTTTGAAACATTGTTTGGTTCAATTTGTAATAT
9856154 TGTGAAAGTTGGTGGACCTATTTAGTAATTATGGAAAATTATGAGATCAATATGTAATTGTTTAA
521 TGTGAAAGTTGGTGGACCTATTTAGTAATTATGGAAAATTATGAGATCAATATGTAATTGTTTAA
9856219 TAGTTGTTGTATTATGTTGGAAATTAATGTTAGATTGTTGAAACTGATGTTAGAATGTGAAATTG
586 TAGTTGTTGTATTATGTTGGAAATTAATGTTAGATTGTTGAAACTGATGTTAGAATGTGAAATTG
9856284 GATTATTTTGGAAAATTGGTCAAAGTTGTGGTTCAAATCACAAATATGGAAAAGTTGGGAACTTA
651 GATTATTTTGGAAAATTGGTCAAAGTTGTGGTTCAAATCACAAATATGGAAAAGTTGGGAACTTA
9856349 AGTGAAAATATTATGTGAATTTTGGATAAATATGAATAAAAAGGAACTTAAATGGTCAATTTGAA
716 AGTGAAAATATTATGTGAATTTTGGATAAATATGAATAAAAAGGAACTTAAATGGTCAATTTGAA
*
9856414 GTGTTAAGGTCAACATTTATGTTGTGACATGAAATTTGTATCGAATGAGCATCGAAATATTTTTA
781 GTGTTAAGGTCAACATTTATGTTGTGACATGAAATTTGTATCGAATGAGCATCGAAAGATTTTTA
9856479 GGAATTTAATTTCTAATGTATGCCTATATCATTAAGATTCTAACATATTTAATTTCTAATGTTTG
846 GGAATTTAATTTCTAATGTATGCCTATATCATTAAGATTCTAACATATTTAATTTCTAATGTTTG
9856544 CCTATGTTAGTAAGGTTTTTAGTAATTTAATTTCTAATGTTTGCCTATTTTTAATTTGTA
911 CCTATGTTAGTAAGGTTTTTAGTAATTTAATTTCTAATGTTTGCCTATTTTTAATTTGTA
9856604 TTTGTGTTAT
Statistics
Matches: 961, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
971 961 1.00
ACGTcount: A:0.33, C:0.08, G:0.20, T:0.39
Consensus pattern (971 bp):
TTTCATTTTTTAGCAATTTCTTTTGGATTTTGGATCAAACCATGAAATAGAAAATTGTTCTATTC
GAAGAGCTCTTTCATTTGGTACCATTATTGCATGCTAATCTTGCTTGAGTGCTAAGATCCCAAAT
TTTAGGGTTTATGTTCATGTTAGGGTTTTATGAATTGATGATGGATTTTGAGGTTATTGAGGTTG
TAGAATCATTTACAAGATTGTTTGATGATCAAAACCACCTAAAAAGATTATTATGATTTTTGGCC
TAAACCCTAAATTAAGGGAAGTTTATGATTTGATGAAATTGAGTTAGGGTTTGATTGTATAGTTT
TAAAATATTGCATAGAGGGTGATTTAATGCTAGAATCAATTGAAATCAAGTGAAAATCATGGAAC
CCTAATCTTTAGACTTTCAGATATGGTTTTAAAAGGTGAGAAAAAATATGGAAATATTATGTAAG
GGTTGGAAATGATGTAGGAATGATTATACAAGCTTTGAAACATTGTTTGGTTCAATTTGTAATAT
TGTGAAAGTTGGTGGACCTATTTAGTAATTATGGAAAATTATGAGATCAATATGTAATTGTTTAA
TAGTTGTTGTATTATGTTGGAAATTAATGTTAGATTGTTGAAACTGATGTTAGAATGTGAAATTG
GATTATTTTGGAAAATTGGTCAAAGTTGTGGTTCAAATCACAAATATGGAAAAGTTGGGAACTTA
AGTGAAAATATTATGTGAATTTTGGATAAATATGAATAAAAAGGAACTTAAATGGTCAATTTGAA
GTGTTAAGGTCAACATTTATGTTGTGACATGAAATTTGTATCGAATGAGCATCGAAAGATTTTTA
GGAATTTAATTTCTAATGTATGCCTATATCATTAAGATTCTAACATATTTAATTTCTAATGTTTG
CCTATGTTAGTAAGGTTTTTAGTAATTTAATTTCTAATGTTTGCCTATTTTTAATTTGTAC
Found at i:9856572 original size:43 final size:42
Alignment explanation
Indices: 9856473--9856591 Score: 139
Period size: 43 Copynumber: 2.8 Consensus size: 42
9856463 CATCGAAATA
* * *
9856473 TTTTTAGGAATTTAATTTCTAATGTATGCCTATATCATTAAG
1 TTTTTAGCAATTTAATTTCTAATGTTTGCCTATATCAGTAAG
* * * * *
9856515 ATTCTAACATATTTAATTTCTAATGTTTGCCTATGTTAGTAAGG
1 TTTTTAGCA-ATTTAATTTCTAATGTTTGCCTATATCAGTAA-G
*
9856559 TTTTTAGTAATTTAATTTCTAATGTTTGCCTAT
1 TTTTTAGCAATTTAATTTCTAATGTTTGCCTAT
9856592 TTTTAATTTG
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 5 0.08
43 52 0.83
44 6 0.10
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.50
Consensus pattern (42 bp):
TTTTTAGCAATTTAATTTCTAATGTTTGCCTATATCAGTAAG
Found at i:9857990 original size:22 final size:22
Alignment explanation
Indices: 9857962--9858004 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
9857952 ACAGTTTATT
*
9857962 ATATATGATGTTTATCATGAAA
1 ATATATGATGTTTACCATGAAA
9857984 ATATATGATGTTTACCATGAA
1 ATATATGATGTTTACCATGAA
9858005 TGTTATTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.14, T:0.40
Consensus pattern (22 bp):
ATATATGATGTTTACCATGAAA
Found at i:9859550 original size:2 final size:2
Alignment explanation
Indices: 9859543--9859597 Score: 57
Period size: 2 Copynumber: 30.0 Consensus size: 2
9859533 TTTATTTATC
* *
9859543 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A AA TA TA AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9859583 T- TA TA TA -A T- TA TA TA
1 TA TA TA TA TA TA TA TA TA
9859598 AATTAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
1 5 0.11
2 40 0.89
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Done.