Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007808.1 Hibiscus syriacus cultivar Beakdansim tig00110129_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: 1698870
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:1184019 original size:20 final size:20
Alignment explanation
Indices: 1183994--1184033 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1183984 GATGGTAAAG
* * *
1183994 GAAGAAGAAGAAGATGAAGA
1 GAAGAAAAACAAGAAGAAGA
1184014 GAAGAAAAACAAGAAGAAGA
1 GAAGAAAAACAAGAAGAAGA
1184034 ATGAGGTAGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.30, T:0.03
Consensus pattern (20 bp):
GAAGAAAAACAAGAAGAAGA
Found at i:1189545 original size:15 final size:15
Alignment explanation
Indices: 1189525--1189732 Score: 229
Period size: 15 Copynumber: 13.5 Consensus size: 15
1189515 TAATAAGGTT
1189525 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
1189540 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
1189555 ATTTATTATAAAATC
1 ATTTATTTTAAAATA
*
1189570 ATTTGTTTTAAAATA
1 ATTTATTTTAAAATA
*
1189585 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1189600 ATTTGTTTTAAAATA
1 ATTTATTTTAAAATA
*
1189615 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
1189630 ATTTGTTTTAAAATA
1 ATTTATTTTAAAATA
** *
1189645 AAATATTATAAAATA
1 ATTTATTTTAAAATA
1189660 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
1189675 AATTATTATAAAATATGAA
1 ATTTATT-TTAAA-AT--A
*
1189694 TTGATTTATTTTAAAAAA
1 ---ATTTATTTTAAAATA
1189712 ATTTA-TTTAAAATA
1 ATTTATTTTAAAATA
1189726 ATTTATT
1 ATTTATT
1189733 AGTATGAATT
Statistics
Matches: 159, Mismatches: 26, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
14 13 0.08
15 127 0.80
16 4 0.03
17 2 0.01
18 1 0.01
19 1 0.01
20 1 0.01
21 4 0.03
22 6 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:1189561 original size:30 final size:30
Alignment explanation
Indices: 1189525--1189732 Score: 265
Period size: 30 Copynumber: 6.7 Consensus size: 30
1189515 TAATAAGGTT
*
1189525 ATTTATTTTAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
* *
1189555 ATTTATTATAAAATCATTTGTTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
*
1189585 ATTTATTATAAAATAATTTGTTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
*
1189615 ATTTATTATAAAATAATTTGTTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
**
1189645 AAATATTATAAAATAATTTATTTTAAAATA
1 ATTTATTATAAAATAATTTATTTTAAAATA
* *
1189675 AATTATTATAAAATATGAATTGATTTATTTTAAAAAA
1 ATTTATTAT-AAA-AT--A---ATTTATTTTAAAATA
1189712 ATTTATT-TAAAATAATTTATT
1 ATTTATTATAAAATAATTTATT
1189733 AGTATGAATT
Statistics
Matches: 161, Mismatches: 10, Indels: 15
0.87 0.05 0.08
Matches are distributed among these distances:
29 7 0.04
30 121 0.75
31 3 0.02
32 3 0.02
34 3 0.02
35 3 0.02
36 1 0.01
37 20 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.49
Consensus pattern (30 bp):
ATTTATTATAAAATAATTTATTTTAAAATA
Found at i:1189708 original size:22 final size:22
Alignment explanation
Indices: 1189677--1189777 Score: 82
Period size: 22 Copynumber: 4.5 Consensus size: 22
1189667 TTAAAATAAA
*
1189677 TTATTATAAAATATGAATTGAT
1 TTATTTTAAAATATGAATTGAT
*
1189699 TTATTTTAAAA-A--AATTTAT
1 TTATTTTAAAATATGAATTGAT
* *
1189718 TTAAAATAATTTATTAGTATGAATTGAT
1 TT---AT--TTTA-AAATATGAATTGAT
*
1189746 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGAATTGAT
1189768 TTATTTTAAA
1 TTATTTTAAA
1189778 CAATTTATTA
Statistics
Matches: 62, Mismatches: 8, Indels: 18
0.70 0.09 0.20
Matches are distributed among these distances:
19 8 0.13
21 1 0.02
22 33 0.53
23 4 0.06
24 4 0.06
25 3 0.05
26 1 0.02
28 8 0.13
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.50
Consensus pattern (22 bp):
TTATTTTAAAATATGAATTGAT
Found at i:1189783 original size:54 final size:54
Alignment explanation
Indices: 1189712--1189880 Score: 268
Period size: 54 Copynumber: 3.1 Consensus size: 54
1189702 TTTTAAAAAA
*
1189712 ATTTATTTAAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
* ** *
1189766 ATTTATTTTAAACAATTTATTAGTAT-ATATTGATTTATTTTAAAATACAGATTT
1 ATTTATTTTAAATAATTTATTAGTATGA-ATTGATTTATTTTAAAATATGGATTG
*
1189820 ATTTATTTTAAATAATTTATTAGTGTGAATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
1189874 ATTTATT
1 ATTTATT
1189881 ATTGTAGTTG
Statistics
Matches: 103, Mismatches: 10, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 101 0.98
55 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.09, T:0.52
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTG
Found at i:1189905 original size:134 final size:134
Alignment explanation
Indices: 1189757--1190014 Score: 426
Period size: 134 Copynumber: 1.9 Consensus size: 134
1189747 TATTTTAAAA
* *
1189757 TATGGATTGATTTATTTTAAACAATTTATTAGTATATATTGATTTATTTTAAAATACAGATTTAT
1 TATGGATTGATTTATTTTAAACAATTTATTAGTATAGATTGATTTATTTTAAAATACAGATTGAT
** *
1189822 TTATTTTAAATAATTTATTAGTGTGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTA
66 TTATTTTAAATAATTTATTAGCATGAATTGATTTATTTTAAAATATAGATTGATTTATTATTGTA
1189887 GTTG
131 GTTG
* * **
1189891 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAACAATTTATTAGTATAGATTGATTTATTTTAAAATACAGATTGAT
*
1189956 TTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAATATAGATTGATTTATT
66 TTATTTTAAATAATTTATTAGCATGAATTGATTTATTTTAAAATATAGATTGATTTATT
1190015 TTAAATAATT
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
134 114 1.00
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAACAATTTATTAGTATAGATTGATTTATTTTAAAATACAGATTGAT
TTATTTTAAATAATTTATTAGCATGAATTGATTTATTTTAAAATATAGATTGATTTATTATTGTA
GTTG
Found at i:1189931 original size:32 final size:32
Alignment explanation
Indices: 1189890--1189997 Score: 137
Period size: 32 Copynumber: 3.7 Consensus size: 32
1189880 TATTGTAGTT
1189890 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1189922 GTATGGATTGATTTA-TTT---TAA---A--A
1 GTATGGATTGATTTATTTTAAATAATTTATTA
1189945 -TATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
1189976 GCATGGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
1189998 ATATAGATTG
Statistics
Matches: 65, Mismatches: 1, Indels: 20
0.76 0.01 0.23
Matches are distributed among these distances:
22 14 0.22
23 4 0.06
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 4 0.06
32 35 0.54
ACGTcount: A:0.34, C:0.01, G:0.14, T:0.51
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:1189948 original size:22 final size:22
Alignment explanation
Indices: 1189923--1189965 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
1189913 AATTTATTAG
1189923 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
1189945 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
1189966 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:1189960 original size:54 final size:54
Alignment explanation
Indices: 1189891--1190029 Score: 260
Period size: 54 Copynumber: 2.6 Consensus size: 54
1189881 ATTGTAGTTG
*
1189891 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAA
1189945 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAA
*
1189999 TATAGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAATAATTTATTA
1190030 TTGTAGTTGT
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 83 1.00
ACGTcount: A:0.36, C:0.01, G:0.12, T:0.52
Consensus pattern (54 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGCATGGATTGATTTATTTTAAAA
Found at i:1190079 original size:31 final size:31
Alignment explanation
Indices: 1190044--1190102 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
1190034 AGTTGTATAG
* *
1190044 ATTATTCAAATTTCAGTATTGTAAAACTAAA
1 ATTATTCAAATCTCAGTATTGCAAAACTAAA
*
1190075 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTCAAATCTCAGTATTGCAAAACT
1190103 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (31 bp):
ATTATTCAAATCTCAGTATTGCAAAACTAAA
Found at i:1190255 original size:20 final size:20
Alignment explanation
Indices: 1190230--1190276 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1190220 CTGCAGATGC
1190230 CTGCAGATATGATCCGCAGA
1 CTGCAGATATGATCCGCAGA
*
1190250 CTGCAGATGTGATCCGCAGA
1 CTGCAGATATGATCCGCAGA
1190270 CTGCAGA
1 CTGCAGA
1190277 CGTTTTACCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (20 bp):
CTGCAGATATGATCCGCAGA
Found at i:1191948 original size:55 final size:56
Alignment explanation
Indices: 1191861--1191972 Score: 172
Period size: 55 Copynumber: 2.0 Consensus size: 56
1191851 AACCAACCTT
* * *
1191861 TTGACTGTTGGATAAATTTTCTCACTGCCTAGAAGATTCCTCCTTTTTGGCGTAAAA
1 TTGACTGTTGGAT-AATATTCTCACTGCCTAGAAGATTCATCCATTTTGGCGTAAAA
*
1191918 TTGACTGTTGGAT-ATATTCTCATTGCCTAGAAGATTCATCCATTTTGGCGTAAAA
1 TTGACTGTTGGATAATATTCTCACTGCCTAGAAGATTCATCCATTTTGGCGTAAAA
1191973 CCAAAAACAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
55 38 0.75
57 13 0.25
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.38
Consensus pattern (56 bp):
TTGACTGTTGGATAATATTCTCACTGCCTAGAAGATTCATCCATTTTGGCGTAAAA
Found at i:1195772 original size:164 final size:164
Alignment explanation
Indices: 1195598--1195894 Score: 432
Period size: 164 Copynumber: 1.8 Consensus size: 164
1195588 AAAAAAAATA
* * * * *
1195598 TCGATCCATAACAATATAACAGGTGAAAATATGATAAAACAAGTCTCAAAATTAACAAAACCAGT
1 TCGATCCATAACAATATAACAGGTAAAAATATAATAAAACAAGTCTAAAAAATAACAAAACCAGA
* * * *
1195663 AAAACGATACCGGATATGTTGAAAGTGTCAATACTTTAATATAAGTATCGACACTTTATGAAATT
66 AAAAAGATACCGGATATATTGAAAGTGTCAATAATTTAATATAAGTATAGACACTTTATGAAATT
1195728 AAACTAAAAAGTGTCGACACTTTATGAAAATGTG
131 AAACTAAAAAGTGTCGACACTTTATGAAAATGTG
* * * **
1195762 TCGATCCATAACAATATAACATGTAAAAATATAATAAAACATGTCTAAAAAATGACAAAACTGGA
1 TCGATCCATAACAATATAACAGGTAAAAATATAATAAAACAAGTCTAAAAAATAACAAAACCAGA
* * * *
1195827 AAAAAGATATCGGATATATTGAAAGTGTCGATAATTTAATATAAGTATAGACACTTTATTAATTT
66 AAAAAGATACCGGATATATTGAAAGTGTCAATAATTTAATATAAGTATAGACACTTTATGAAATT
1195892 AAA
131 AAA
1195895 AGAGAAAAAG
Statistics
Matches: 115, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
164 115 1.00
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (164 bp):
TCGATCCATAACAATATAACAGGTAAAAATATAATAAAACAAGTCTAAAAAATAACAAAACCAGA
AAAAAGATACCGGATATATTGAAAGTGTCAATAATTTAATATAAGTATAGACACTTTATGAAATT
AAACTAAAAAGTGTCGACACTTTATGAAAATGTG
Found at i:1196272 original size:183 final size:182
Alignment explanation
Indices: 1195735--1196374 Score: 784
Period size: 183 Copynumber: 3.5 Consensus size: 182
1195725 ATTAAACTAA
* ** * * *
1195735 AAAGTGTCGACACTTTATGAAAATGTGTCGATCCATAACAATATAACATGTAAAAATATAATAAA
1 AAAGTGTCGATACTTTAAAAAAATGTATCGATCCATAATAATATAACAAGTAAAAATATAATAAA
* * * * * * *
1195800 ACATGTCTAAAAAATGACAAAACTGGAAAAAAGATATCGGATATATTGAAAGTGTCGATAATTTA
66 ACAGGTCT-CAAAATGATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATAATTTA
* * * * * * *
1195865 ATATAAGTATAGACACTTTATTAATTTAAAAGAGAAAAAGTTATAGCCCCTAA
130 ATATAAATATCGACACTTTATGAATTTAAAAGAGAAGAAGTTATAACGCCTAT
*** ** * * *
1195918 AAAGTGTCGACGTTTTATGAAAATGTATCGATCTATAATAATATAACAACTAAAAATATGATAAA
1 AAAGTGTCGATACTTTAAAAAAATGTATCGATCCATAATAATATAACAAGTAAAAATATAATAAA
* ** * * * *
1195983 ACCGGTCTCAACAATGA-AAAAGTGATAAAACGATACCGGATATGTTTAAAGTGTCGATACTTTA
66 ACAGGTCTCAA-AATGATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATAATTTA
*
1196047 ATATAACTATCGACACTTT-TGGAATTTAAAAGAGAAGAAGTTATAACGCCTAT
130 ATATAAATATCGACACTTTAT-GAATTTAAAAGAGAAGAAGTTATAACGCCTAT
*
1196100 AAAGTGTCGATACTTTAAAAAAAAT-TATCGATCCATAATAATATAACAGGTAAAAATATAATAA
1 AAAGTGTCGATACTTT-AAAAAAATGTATCGATCCATAATAATATAACAAGTAAAAATATAATAA
* * * *
1196164 AACATGTCTCAAAATTGATAAAACCAGTAAAACGCTACCAGATATATTGAAAGTGTCGATAATTT
65 AACAGGTCTCAAAA-TGATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATAATTT
1196229 AATATAAATATCGACACTTTATGAATTTAAAAGAGAAGAAGTTATAACGCCTAT
129 AATATAAATATCGACACTTTATGAATTTAAAAGAGAAGAAGTTATAACGCCTAT
* * **
1196283 AAAGTGTCGATACTTTTAAAAAATATATTAATCCATAA-AATATAACAAGTAAAAATATAATAAA
1 AAAGTGTCGATACTTTAAAAAAATGTATCGATCCATAATAATATAACAAGTAAAAATATAATAAA
* *
1196347 ACCGGTATCAAAATGATAAAACCGGTAA
66 ACAGGTCTCAAAATGATAAAACCGGTAA
1196375 GCACTACCTA
Statistics
Matches: 395, Mismatches: 55, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
181 17 0.04
182 188 0.48
183 189 0.48
184 1 0.00
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (182 bp):
AAAGTGTCGATACTTTAAAAAAATGTATCGATCCATAATAATATAACAAGTAAAAATATAATAAA
ACAGGTCTCAAAATGATAAAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATAATTTAA
TATAAATATCGACACTTTATGAATTTAAAAGAGAAGAAGTTATAACGCCTAT
Found at i:1196480 original size:23 final size:23
Alignment explanation
Indices: 1196430--1196474 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1196420 TGTCTATTTT
*
1196430 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
1196453 ATTATATAAGCGAC-ACCTAATA
1 ATTATATAAGCG-CTACCTAATA
1196475 TGTTATTGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 19 0.95
24 1 0.05
ACGTcount: A:0.40, C:0.20, G:0.09, T:0.31
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1196518 original size:87 final size:88
Alignment explanation
Indices: 1196372--1196595 Score: 400
Period size: 87 Copynumber: 2.6 Consensus size: 88
1196362 ATAAAACCGG
*
1196372 TAAGC-ACTACCTAATATGTTATTGTACTTAATAATATTTCCGGTTAAATGTCTATTTTATTATA
1 TAAGCGACTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGTCTATTTTATTATA
1196436 TAAGCGCTACCTATTACATTATA
66 TAAGCGCTACCTATTACATTATA
1196459 TAAGCGAC-ACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGTCTATTTTATTATA
1 TAAGCGACTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGTCTATTTTATTATA
1196523 TAAGCGCTACCTATTACATTATA
66 TAAGCGCTACCTATTACATTATA
* *
1196546 TAAGCG-CTACCTAATATGTTATTGTGCTTGATAATATTTCTGGTTAAATG
1 TAAGCGACTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATG
1196596 ATATAACATA
Statistics
Matches: 132, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
86 1 0.01
87 129 0.98
88 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (88 bp):
TAAGCGACTACCTAATATGTTATTGTACTTGATAATATTTCCGGTTAAATGTCTATTTTATTATA
TAAGCGCTACCTATTACATTATA
Found at i:1196567 original size:23 final size:23
Alignment explanation
Indices: 1196517--1196561 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1196507 TGTCTATTTT
*
1196517 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
1196540 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1196562 TGTTATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1197132 original size:16 final size:16
Alignment explanation
Indices: 1197103--1197145 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1197093 ATATTAAAAC
1197103 ATTA-ATTTTT-TTAA
1 ATTATATTTTTATTAA
1197117 ATTATATTTTTATTAA
1 ATTATATTTTTATTAA
*
1197133 ATAATATTATTTA
1 ATTATATT-TTTA
1197146 ATAATACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 4 0.16
15 6 0.24
16 11 0.44
17 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTATATTTTTATTAA
Found at i:1197904 original size:60 final size:60
Alignment explanation
Indices: 1197831--1197958 Score: 202
Period size: 60 Copynumber: 2.1 Consensus size: 60
1197821 GTATCCAATT
* *
1197831 AACACATACTTACACCAGTGTAAGTATGTACATCTCCCAATATCTTGATACCTGAAAATA
1 AACACATACTTACACCAGTGTAAATATGTACATCTCCCAATATCTTGATACCTAAAAATA
* * *
1197891 AACATATACTTACACCAGTGTAAATATGTACATCTCCCAATATCTTTATACTTAAAAATA
1 AACACATACTTACACCAGTGTAAATATGTACATCTCCCAATATCTTGATACCTAAAAATA
*
1197951 ATCACATA
1 AACACATA
1197959 ACTATATTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 61 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.30
Consensus pattern (60 bp):
AACACATACTTACACCAGTGTAAATATGTACATCTCCCAATATCTTGATACCTAAAAATA
Found at i:1198603 original size:47 final size:47
Alignment explanation
Indices: 1198550--1198646 Score: 133
Period size: 47 Copynumber: 2.1 Consensus size: 47
1198540 ATGCAAGTGA
* * *
1198550 TCATAACACTAACATTCATCCTACATCATC-AATCTTCAGCATTTGCT
1 TCATAACACTAACATTCATCATACAT-AACAAATCTTCAGCATTCGCT
* *
1198597 TCATAACATTAACATTCATCATGCATAACAAATCTTCAGCATTCGCT
1 TCATAACACTAACATTCATCATACATAACAAATCTTCAGCATTCGCT
1198644 TCA
1 TCA
1198647 GTCTTTTACT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
46 2 0.05
47 42 0.95
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (47 bp):
TCATAACACTAACATTCATCATACATAACAAATCTTCAGCATTCGCT
Found at i:1202892 original size:3 final size:3
Alignment explanation
Indices: 1202884--1202925 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
1202874 TTAAAACTCT
1202884 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1202926 CTCCTGTATC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:1204187 original size:31 final size:31
Alignment explanation
Indices: 1204149--1204208 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1204139 GAGTCGAGGG
1204149 TTACCTATGTTCTACGGAACATATGGACAAT
1 TTACCTATGTTCTACGGAACATATGGACAAT
*
1204180 TTACCTATGTTCTTCGGAACATATGGACA
1 TTACCTATGTTCTACGGAACATATGGACA
1204209 GTTACATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (31 bp):
TTACCTATGTTCTACGGAACATATGGACAAT
Found at i:1204226 original size:30 final size:31
Alignment explanation
Indices: 1204148--1204219 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
1204138 AGAGTCGAGG
* *
1204148 GTTACCTATGTTCTACGGAACATATGGACAA
1 GTTACATATGTTCTTCGGAACATATGGACAA
* *
1204179 TTTACCTATGTTCTTCGGAACATATGGAC-A
1 GTTACATATGTTCTTCGGAACATATGGACAA
1204209 GTTACATATGT
1 GTTACATATGT
1204220 CATTCGGGAC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 10 0.27
31 27 0.73
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (31 bp):
GTTACATATGTTCTTCGGAACATATGGACAA
Found at i:1206275 original size:47 final size:47
Alignment explanation
Indices: 1206221--1206310 Score: 162
Period size: 47 Copynumber: 1.9 Consensus size: 47
1206211 ATGCACATGA
*
1206221 TCATAACACTAACATTCATCCTACATCATCAATCTTCAGCATTTGCT
1 TCATAACACTAACATTCATCCTACATCACCAATCTTCAGCATTTGCT
*
1206268 TCATAACACTAACATTCATCCTGCATCACCAATCTTCAGCATT
1 TCATAACACTAACATTCATCCTACATCACCAATCTTCAGCATT
1206311 CGTTTCAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.32, C:0.31, G:0.04, T:0.32
Consensus pattern (47 bp):
TCATAACACTAACATTCATCCTACATCACCAATCTTCAGCATTTGCT
Found at i:1206503 original size:29 final size:28
Alignment explanation
Indices: 1206422--1206506 Score: 86
Period size: 27 Copynumber: 3.0 Consensus size: 28
1206412 TAATATTTTA
* *
1206422 AAATAATTAAAATAATATATTTTATAAT
1 AAATAGTTAAATTAATATATTTTATAAT
* *
1206450 AATATAGTTATAATT-AT-T-TATTATATT
1 AA-ATAGTTA-AATTAATATATTTTATAAT
1206477 CAAATAGTTAAATTAATATATTTTATAAT
1 -AAATAGTTAAATTAATATATTTTATAAT
1206506 A
1 A
1206507 TATTTTATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
26 4 0.09
27 16 0.36
28 7 0.16
29 15 0.33
30 3 0.07
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (28 bp):
AAATAGTTAAATTAATATATTTTATAAT
Found at i:1206505 original size:12 final size:12
Alignment explanation
Indices: 1206490--1206515 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1206480 ATAGTTAAAT
1206490 TAATATATTTTA
1 TAATATATTTTA
1206502 TAATATATTTTA
1 TAATATATTTTA
1206514 TA
1 TA
1206516 TTTTTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TAATATATTTTA
Found at i:1206565 original size:28 final size:26
Alignment explanation
Indices: 1206512--1206569 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
1206502 TAATATATTT
*
1206512 TATATTTTTAATAAATAAATAAAAAA
1 TATATTTTTAATAAATAAAAAAAAAA
1206538 TATA-TTTTAATAATATAAAAAATTAAAA
1 TATATTTTTAATAA-ATAAAAAA--AAAA
1206566 TATA
1 TATA
1206570 ATACATGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 9 0.32
26 11 0.39
28 8 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TATATTTTTAATAAATAAAAAAAAAA
Found at i:1207615 original size:17 final size:17
Alignment explanation
Indices: 1207589--1207625 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1207579 TTTTATTGGT
*
1207589 TTAAAATTAGTTGATAA
1 TTAAAATTAGTTAATAA
*
1207606 TTAAATTTAGTTAATAA
1 TTAAAATTAGTTAATAA
1207623 TTA
1 TTA
1207626 TTATGAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (17 bp):
TTAAAATTAGTTAATAA
Found at i:1208649 original size:89 final size:89
Alignment explanation
Indices: 1208498--1208676 Score: 295
Period size: 89 Copynumber: 2.0 Consensus size: 89
1208488 TCTATAGAGA
** *
1208498 GAGGATGTCTTAGTCTTTAAAATTATGCGATTATTAGTTTGGAGAGATGTAATACTTTTGTAGTC
1 GAGGATGTCTTAGTCTTTAAAATTATGAAATTATTAGTTTGGAGAAATGTAATACTTTTGTAGTC
*
1208563 TTTATAACCTTTGGAGTTTATTTT
66 TCTATAACCTTTGGAGTTTATTTT
* *
1208587 GAGGATGTCTTAGTCTTTAAAATTATGAAATTATTAGTTTGGATAAATGTAATCCTTTTGTAGTC
1 GAGGATGTCTTAGTCTTTAAAATTATGAAATTATTAGTTTGGAGAAATGTAATACTTTTGTAGTC
*
1208652 TCTATAATCTTTGGAGTTTATTTT
66 TCTATAACCTTTGGAGTTTATTTT
1208676 G
1 G
1208677 CATAGATGAA
Statistics
Matches: 83, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.46
Consensus pattern (89 bp):
GAGGATGTCTTAGTCTTTAAAATTATGAAATTATTAGTTTGGAGAAATGTAATACTTTTGTAGTC
TCTATAACCTTTGGAGTTTATTTT
Found at i:1209695 original size:18 final size:18
Alignment explanation
Indices: 1209672--1209706 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1209662 AAATACTAAT
1209672 AATAAATTATTT-TTTATC
1 AATAAA-TATTTATTTATC
1209690 AATAAATATTTATTTAT
1 AATAAATATTTATTTAT
1209707 TTTTGGGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
AATAAATATTTATTTATC
Found at i:1225260 original size:20 final size:20
Alignment explanation
Indices: 1225235--1225273 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1225225 TCTTTCTCTT
1225235 GAGAGAGAAGCTCTCCCTTA
1 GAGAGAGAAGCTCTCCCTTA
1225255 GAGAGAGAAGCTCTCCCTT
1 GAGAGAGAAGCTCTCCCTT
1225274 CTCTCTAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (20 bp):
GAGAGAGAAGCTCTCCCTTA
Found at i:1226293 original size:23 final size:24
Alignment explanation
Indices: 1226251--1226301 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1226241 TCCAGGGGCG
*
1226251 CATAGAATTTGTCCCCAAGGACCA
1 CATAGAATATGTCCCCAAGGACCA
* *
1226275 CATAGAA-ATGTCCCGAAGGACTA
1 CATAGAATATGTCCCCAAGGACCA
1226298 CATA
1 CATA
1226302 TAACACATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (24 bp):
CATAGAATATGTCCCCAAGGACCA
Found at i:1226406 original size:21 final size:21
Alignment explanation
Indices: 1226380--1226419 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1226370 CCGAAGTACC
*
1226380 ACATATATGTTCCAAAGGATT
1 ACATATATGTCCCAAAGGATT
*
1226401 ACATATATGTCCCGAAGGA
1 ACATATATGTCCCAAAGGA
1226420 CCACGTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
ACATATATGTCCCAAAGGATT
Found at i:1227471 original size:16 final size:18
Alignment explanation
Indices: 1227439--1227471 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1227429 ACCCGAAAAG
1227439 TTTCCATATCTTATTAAA
1 TTTCCATATCTTATTAAA
1227457 TTTCCAT-TC-TATTAA
1 TTTCCATATCTTATTAA
1227472 CTTCTTTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.30, C:0.18, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTCCATATCTTATTAAA
Found at i:1230485 original size:21 final size:21
Alignment explanation
Indices: 1230459--1230498 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1230449 CCGAAGTACC
*
1230459 ACATATATGTTCCAAAGGATT
1 ACATATATGTCCCAAAGGATT
*
1230480 ACATATATGTCCCGAAGGA
1 ACATATATGTCCCAAAGGA
1230499 CCACGTAGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (21 bp):
ACATATATGTCCCAAAGGATT
Found at i:1232797 original size:20 final size:21
Alignment explanation
Indices: 1232756--1232802 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
1232746 AAACTAGTAA
1232756 TTGGGCCTCCGAGTTTTGTAT
1 TTGGGCCTCCGAGTTTTGTAT
*
1232777 TTGGGCC-CCGA-TTTATTTAT
1 TTGGGCCTCCGAGTTT-TGTAT
1232797 TTGGGC
1 TTGGGC
1232803 TTATAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 3 0.12
20 14 0.58
21 7 0.29
ACGTcount: A:0.11, C:0.19, G:0.28, T:0.43
Consensus pattern (21 bp):
TTGGGCCTCCGAGTTTTGTAT
Found at i:1232853 original size:3 final size:3
Alignment explanation
Indices: 1232847--1232893 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
1232837 TACTACTAAC
* *
1232847 AAT AAT AGT AAT -AT AAT AAT AAT AAT AGT AAT -AT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1232893 A
1 A
1232894 TAAATATGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 4 0.11
3 34 0.89
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1232866 original size:14 final size:13
Alignment explanation
Indices: 1232855--1232896 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 13
1232845 ACAATAATAG
1232855 TAATATAATAATAA
1 TAATATAAT-ATAA
1232869 TAATAGTAATATAA
1 TAATA-TAATATAA
1232883 TAATAATAATATAA
1 TAAT-ATAATATAA
1232897 ATATGTAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (13 bp):
TAATATAATATAA
Found at i:1232900 original size:20 final size:20
Alignment explanation
Indices: 1232847--1232893 Score: 94
Period size: 20 Copynumber: 2.4 Consensus size: 20
1232837 TACTACTAAC
1232847 AATAATAGTAATATAATAAT
1 AATAATAGTAATATAATAAT
1232867 AATAATAGTAATATAATAAT
1 AATAATAGTAATATAATAAT
1232887 AATAATA
1 AATAATA
1232894 TAAATATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (20 bp):
AATAATAGTAATATAATAAT
Found at i:1233137 original size:42 final size:42
Alignment explanation
Indices: 1233070--1233161 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
1233060 GAATGGCACT
* * * *
1233070 AAGGATTT-ATCATCTTGCTCAAAAGACTGATAGATGACCCT
1 AAGGATTTAAGCATCATGCTCAAAAGACTGACAGATGACCCG
* *
1233111 AAGGTTTTAAGCATCATGCTCGAAAGACTGACAGATGACCCG
1 AAGGATTTAAGCATCATGCTCAAAAGACTGACAGATGACCCG
1233153 AAGGATTTA
1 AAGGATTTA
1233162 CAAATTTGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 7 0.16
42 36 0.84
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (42 bp):
AAGGATTTAAGCATCATGCTCAAAAGACTGACAGATGACCCG
Found at i:1233385 original size:42 final size:42
Alignment explanation
Indices: 1233303--1233409 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 42
1233293 ACCCAAAGGT
* * * * *
1233303 CTGACGGATGGCCCTAAAGACTT-ATCATCTTGCTCAAAAGA
1 CTGACAGATGACCCTAAAGATTTAAGCATCATGCTCAAAAGA
* *
1233344 CTGATAGATGACCCTAAAGATTTAAGCATCATGCTCGAAAGA
1 CTGACAGATGACCCTAAAGATTTAAGCATCATGCTCAAAAGA
* *
1233386 CTGACAGATGACCCGAATGATTTA
1 CTGACAGATGACCCTAAAGATTTA
1233410 CAAATTTGTG
Statistics
Matches: 55, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
41 19 0.35
42 36 0.65
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (42 bp):
CTGACAGATGACCCTAAAGATTTAAGCATCATGCTCAAAAGA
Found at i:1233483 original size:248 final size:248
Alignment explanation
Indices: 1233036--1233513 Score: 780
Period size: 248 Copynumber: 1.9 Consensus size: 248
1233026 CAAAAGTAAA
* * *
1233036 AAACATCCTACCCAAAGGTATGACGAATGGCACTAAGGATTTATCATCTTGCTCAAAAGACTGAT
1 AAACATACTACCCAAAGGTATGACGAATGGCACTAAAGACTTATCATCTTGCTCAAAAGACTGAT
* *
1233101 AGATGACCCTAAGGTTTTAAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAA
66 AGATGACCCTAAAGATTTAAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAA
* *
1233166 TTTGTGGGAAATAATTTACTGGGTAAAAAACTTCTTACTTTTCAAAAATTTCATTTCTTGAACAT
131 TTTGTGGGAAATAATTTACTGGGTAAAAAACTTCTTACTTTTCAAAAATTTCATTTATAGAACAT
1233231 TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAATCATGTGT
196 TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAATCATGTGT
* * *
1233284 AAACATACTACCCAAAGGTCTGACGGATGGCCCTAAAGACTTATCATCTTGCTCAAAAGACTGAT
1 AAACATACTACCCAAAGGTATGACGAATGGCACTAAAGACTTATCATCTTGCTCAAAAGACTGAT
*
1233349 AGATGACCCTAAAGATTTAAGCATCATGCTCGAAAGACTGACAGATGACCCGAATGATTTACAAA
66 AGATGACCCTAAAGATTTAAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAA
* * *
1233414 TTTGTGGGAAATAATTTACTGGGTAAGACA-TTCTTACTTTTCAAAAATTTCA-TTATAGAAAAG
131 TTTGTGGGAAATAATTTACTGGGTAAAAAACTTCTTACTTTTCAAAAATTTCATTTATAG--AAC
* *
1233477 ATTAAATGAGAAACTTTGAAAATTGTTTTCTCATTTT
194 ATTAAATGAGAAACTTTGAAAATCGCTTTCTCATTTT
1233514 TCAAAATAAA
Statistics
Matches: 212, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
246 4 0.02
247 22 0.10
248 186 0.88
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (248 bp):
AAACATACTACCCAAAGGTATGACGAATGGCACTAAAGACTTATCATCTTGCTCAAAAGACTGAT
AGATGACCCTAAAGATTTAAGCATCATGCTCGAAAGACTGACAGATGACCCGAAGGATTTACAAA
TTTGTGGGAAATAATTTACTGGGTAAAAAACTTCTTACTTTTCAAAAATTTCATTTATAGAACAT
TAAATGAGAAACTTTGAAAATCGCTTTCTCATTTTCATGCGAAAATCATGTGT
Found at i:1242347 original size:3 final size:3
Alignment explanation
Indices: 1242339--1242398 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
1242329 TTTATTTGGG
* * * *
1242339 ATA ATA ATA ATA TTA TTA TTTA ATA ATA ATA ATA ATA ATA GTA AT-
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA
1242384 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
1242399 TAAATATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
ATA
Found at i:1242354 original size:25 final size:22
Alignment explanation
Indices: 1242339--1242395 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1242329 TTTATTTGGG
1242339 ATAATAATAATATTATTATTTA
1 ATAATAATAATATTATTATTTA
* * * *
1242361 ATAATAATAATAATAATAGTAA
1 ATAATAATAATATTATTATTTA
1242383 TATAATAATAATA
1 -ATAATAATAATA
1242396 ATATAAATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 18 0.60
23 12 0.40
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAATAATAATATTATTATTTA
Found at i:1242406 original size:20 final size:20
Alignment explanation
Indices: 1242359--1242398 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 20
1242349 TATTATTATT
1242359 TAATAATAATAATAATAATAG
1 TAAT-ATAATAATAATAATAG
1242380 TAATATAATAATAATAATA
1 TAATATAATAATAATAATA
1242399 TAAATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (20 bp):
TAATATAATAATAATAATAG
Found at i:1247675 original size:54 final size:54
Alignment explanation
Indices: 1247634--1247987 Score: 428
Period size: 54 Copynumber: 6.6 Consensus size: 54
1247624 TAAACCTATT
*
1247634 ATGAATTTCGTGAAATGCACACTTAGTACCGAAACGTTTATTCATCCACATAGG
1 ATGAATTTCGTGAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGG
* * * ** * * *
1247688 A-CAAATTCTGTTAAATGCACACTTAGTGCTAAAACGGTCATTCATCCACATAGA
1 ATGAATTTC-GTGAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGG
* *
1247742 ATGAA-TTCTTTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGG
1 ATGAATTTC-GTGAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGG
* * * * * * *
1247796 ACGAATTCCGTGAAATACATACTTATTGCTGAAACGGTTATTCATCCACATAGG
1 ATGAATTTCGTGAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGG
* *
1247850 ATGAATTACGTGAAATGCACTCTTAGTGCCGAAAC-TATTATTCATCCACATAGG
1 ATGAATTTCGTGAAATGCACACTTAGTGCCGAAACGT-TTATTCATCCACATAGG
* * *
1247904 ATGAATTTCGTGAAATGCATAGTTAGTGCTGAAACGTTTATTCATCCACATAGG
1 ATGAATTTCGTGAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGG
*
1247958 ATGAA-TTCTGTGAAATGCACATTTAGTGCC
1 ATGAATTTC-GTGAAATGCACACTTAGTGCC
1247988 TATTTGGTAA
Statistics
Matches: 253, Mismatches: 41, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
53 8 0.03
54 240 0.95
55 5 0.02
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (54 bp):
ATGAATTTCGTGAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGG
Found at i:1247783 original size:108 final size:108
Alignment explanation
Indices: 1247634--1247987 Score: 498
Period size: 108 Copynumber: 3.3 Consensus size: 108
1247624 TAAACCTATT
* * *
1247634 ATGAATT-TCGTGAAATGCACACTTAGTACCGAAACGTTTATTCATCCACATAGGACAAATTCTG
1 ATGAATTCT-GTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGGACGAATTCTG
* * * * *
1247698 TTAAATGCACACTTAGTGCTAAAACGGTCATTCATCCACATAGA
65 TGAAATGCATACTTAGTGCTGAAACGGTTATTCATCCACATAGG
* *
1247742 ATGAATTCTTTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGGACGAATTCCGT
1 ATGAATTCTGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGGACGAATTCTGT
* *
1247807 GAAATACATACTTATTGCTGAAACGGTTATTCATCCACATAGG
66 GAAATGCATACTTAGTGCTGAAACGGTTATTCATCCACATAGG
* * *
1247850 ATGAATTAC-GTGAAATGCACTCTTAGTGCCGAAACTATTATTCATCCACATAGGATGAATT-TC
1 ATGAATT-CTGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGGACGAATTCT-
* *
1247913 GTGAAATGCATAGTTAGTGCTGAAACGTTTATTCATCCACATAGG
64 GTGAAATGCATACTTAGTGCTGAAACGGTTATTCATCCACATAGG
*
1247958 ATGAATTCTGTGAAATGCACATTTAGTGCC
1 ATGAATTCTGTGAAATGCACACTTAGTGCC
1247988 TATTTGGTAA
Statistics
Matches: 219, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
107 1 0.00
108 216 0.99
109 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.30
Consensus pattern (108 bp):
ATGAATTCTGTGAAATGCACACTTAGTGCCGAAACGATTATTCATCCACATAGGACGAATTCTGT
GAAATGCATACTTAGTGCTGAAACGGTTATTCATCCACATAGG
Found at i:1253663 original size:54 final size:54
Alignment explanation
Indices: 1253604--1254276 Score: 806
Period size: 54 Copynumber: 12.3 Consensus size: 54
1253594 ATTTCTTTAT
* ** * **
1253604 AAATGCAC-CTATAGTGCTCATACGGTTATTCATAAACCTATTATGAATTCCGTG
1 AAATGCACACT-TAGTGCTCAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* *
1253658 AAATGCACACTTAGTG-TCGAAACGGTTATTCATTCACATAGGATGAATTTCGTG
1 AAATGCACACTTAGTGCTC-AAACGGTTATTCATCCACATAGGATGAATTCCGTG
* *
1253712 AAATGCACACTTAGTGCCCAAACGTTTATTCATCCACATAGGATGAATTCCGTG
1 AAATGCACACTTAGTGCTCAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* *
1253766 AAATGCACACTTAGCGCTGAAACGGTTATTCATCCACATAGGATGAATTCCGTG
1 AAATGCACACTTAGTGCTCAAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * * *
1253820 AAATATACACTTGCACAATTAGTTC-CAAAACAGTTATTCATCCACATAGGACGAATTCCGTG
1 ----A-A-A--TGCACACTTAGTGCTC-AAACGGTTATTCATCCACATAGGATGAATTCCGTG
* *
1253882 AAATGCACACTTAATGC-CAAAACGGCTATTCATCCACATAGGATGAATTCCGTG
1 AAATGCACACTTAGTGCTC-AAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * *
1253936 AAATGCACACTTAGTGC-CGAAACGATTATTCATTCACATAGGATGACTTCCGTG
1 AAATGCACACTTAGTGCTC-AAACGGTTATTCATCCACATAGGATGAATTCCGTG
* **
1253990 AAATGCAAACTTAGTGC-CGAAACGGTTATTCATCCACATAGGATGAATTTTGTG
1 AAATGCACACTTAGTGCTC-AAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * * *
1254044 AAATGAACACTTAGTGC-CGAAATGTTTATTCATCCACATAGGATGAATTCTGTG
1 AAATGCACACTTAGTGCTC-AAACGGTTATTCATCCACATAGGATGAATTCCGTG
*
1254098 AAATGCACACTTAGTGC-CGAAACGGTTATTCATCCACATAGGATGAATTCCATG
1 AAATGCACACTTAGTGCTC-AAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * *
1254152 AAATACACACTTAGTTC-CAAAACGGTTATTCATCCACATAGGATTAATTCCGTG
1 AAATGCACACTTAGTGCTC-AAACGGTTATTCATCCACATAGGATGAATTCCGTG
* * * *
1254206 AAATGCACACTTAGTGCTGAAACGTTTATTCATCCACATATGATGAATTCTGTG
1 AAATGCACACTTAGTGCTCAAACGGTTATTCATCCACATAGGATGAATTCCGTG
1254260 AAATGCACACTTAGTGC
1 AAATGCACACTTAGTGC
1254277 CTATTTGGTA
Statistics
Matches: 545, Mismatches: 61, Indels: 26
0.86 0.10 0.04
Matches are distributed among these distances:
53 2 0.00
54 490 0.90
55 3 0.01
56 1 0.00
57 1 0.00
58 2 0.00
59 1 0.00
60 1 0.00
62 44 0.08
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (54 bp):
AAATGCACACTTAGTGCTCAAACGGTTATTCATCCACATAGGATGAATTCCGTG
Found at i:1254109 original size:162 final size:162
Alignment explanation
Indices: 1253646--1254277 Score: 888
Period size: 162 Copynumber: 3.9 Consensus size: 162
1253636 TAAACCTATT
* * * * *
1253646 ATGAATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATTCACATAGGATGAATTTCGT
1 ATGAATTCCGTGAAATGCAAACTTAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGT
*
1253711 GAAATGCACACTTAGTGCCCAAACGTTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC
66 GAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC
* *
1253776 TTAGCGCTGAAACGGTTATTCATCCACATAGG
131 TTAGTGCCGAAACGGTTATTCATCCACATAGG
* * *
1253808 ATGAATTCCGTGAAATATACACTTGCACAA-TTAGTTCCAAAACAGTTATTCATCCACATAGGAC
1 ATGAATTCCGTG----A-A-A--TGCA-AACTTAGTGCCAAAACGGTTATTCATCCACATAGGAT
* * **
1253872 GAATTCCGTGAAATGCACACTTAATGCCAAAACGGCTATTCATCCACATAGGATGAATTCCGTGA
57 GAATTCCGTGAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGGATGAATTCCGTGA
* *
1253937 AATGCACACTTAGTGCCGAAACGATTATTCATTCACATAGG
122 AATGCACACTTAGTGCCGAAACGGTTATTCATCCACATAGG
* * **
1253978 ATGACTTCCGTGAAATGCAAACTTAGTGCCGAAACGGTTATTCATCCACATAGGATGAATTTTGT
1 ATGAATTCCGTGAAATGCAAACTTAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGT
* * *
1254043 GAAATGAACACTTAGTGCCGAAATGTTTATTCATCCACATAGGATGAATTCTGTGAAATGCACAC
66 GAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC
1254108 TTAGTGCCGAAACGGTTATTCATCCACATAGG
131 TTAGTGCCGAAACGGTTATTCATCCACATAGG
* * * * *
1254140 ATGAATTCCATGAAATACACACTTAGTTCCAAAACGGTTATTCATCCACATAGGATTAATTCCGT
1 ATGAATTCCGTGAAATGCAAACTTAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGT
* * *
1254205 GAAATGCACACTTAGTGCTGAAACGTTTATTCATCCACATATGATGAATTCTGTGAAATGCACAC
66 GAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC
1254270 TTAGTGCC
131 TTAGTGCC
1254278 TATTTGGTAA
Statistics
Matches: 415, Mismatches: 45, Indels: 20
0.86 0.09 0.04
Matches are distributed among these distances:
161 2 0.00
162 266 0.64
164 1 0.00
165 1 0.00
166 2 0.00
167 1 0.00
168 1 0.00
170 140 0.34
171 1 0.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (162 bp):
ATGAATTCCGTGAAATGCAAACTTAGTGCCAAAACGGTTATTCATCCACATAGGATGAATTCCGT
GAAATGCACACTTAGTGCCGAAACGTTTATTCATCCACATAGGATGAATTCCGTGAAATGCACAC
TTAGTGCCGAAACGGTTATTCATCCACATAGG
Found at i:1254644 original size:22 final size:22
Alignment explanation
Indices: 1254612--1254655 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1254602 GTATCGATAC
*
1254612 CCATACCATGGTATCAATACTA
1 CCATACCATGGTACCAATACTA
* *
1254634 CCATACTATGGTACCGATACTA
1 CCATACCATGGTACCAATACTA
1254656 TGCTATGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (22 bp):
CCATACCATGGTACCAATACTA
Found at i:1260755 original size:21 final size:21
Alignment explanation
Indices: 1260722--1260780 Score: 82
Period size: 21 Copynumber: 2.8 Consensus size: 21
1260712 ATTATCCAAT
*
1260722 AAACTTGACATCCATAACAAC
1 AAACTTGAAATCCATAACAAC
* *
1260743 AAATTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAC
*
1260764 ACACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
1260781 TAATAAATCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.22
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAC
Found at i:1262573 original size:40 final size:41
Alignment explanation
Indices: 1262528--1262631 Score: 131
Period size: 40 Copynumber: 2.6 Consensus size: 41
1262518 AAAGACTGAA
* *
1262528 TATTTAGCGGCGTTTGTATACAAACACCACTAAAGTA-TAG
1 TATTTAGCGGCGTTTGTATAAAAACACCACTAAAGTACAAG
* * **
1262568 TATTTAGTGGCGTTTATATAAAAATGCCACTAAAGTACAAG
1 TATTTAGCGGCGTTTGTATAAAAACACCACTAAAGTACAAG
*
1262609 TATTTACCGGCGTTTGT-TAAAAA
1 TATTTAGCGGCGTTTGTATAAAAA
1262632 AAAAGGCAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
40 38 0.70
41 16 0.30
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (41 bp):
TATTTAGCGGCGTTTGTATAAAAACACCACTAAAGTACAAG
Found at i:1274956 original size:21 final size:21
Alignment explanation
Indices: 1274930--1274992 Score: 126
Period size: 21 Copynumber: 3.0 Consensus size: 21
1274920 TATGCTCTTT
1274930 GATACATGTTGATAATGAATA
1 GATACATGTTGATAATGAATA
1274951 GATACATGTTGATAATGAATA
1 GATACATGTTGATAATGAATA
1274972 GATACATGTTGATAATGAATA
1 GATACATGTTGATAATGAATA
1274993 AATATATGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.33
Consensus pattern (21 bp):
GATACATGTTGATAATGAATA
Found at i:1279246 original size:20 final size:20
Alignment explanation
Indices: 1279221--1279260 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
1279211 ACCCGTTAAC
*
1279221 CCGTTGACCGCCGTTGACTA
1 CCGTTGACCACCGTTGACTA
*
1279241 CCGTTGACCATCGTTGACTA
1 CCGTTGACCACCGTTGACTA
1279261 GAATTTTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.17, C:0.33, G:0.23, T:0.28
Consensus pattern (20 bp):
CCGTTGACCACCGTTGACTA
Found at i:1283567 original size:13 final size:13
Alignment explanation
Indices: 1283533--1283578 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
1283523 GACCCGACCT
*
1283533 GACCCGACTACCC
1 GACCCGACTGCCC
1283546 GACCC-ACTGCCC
1 GACCCGACTGCCC
*
1283558 GACCCGACTGCCT
1 GACCCGACTGCCC
1283571 GACCCGAC
1 GACCCGAC
1283579 CCGTTAACCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.20, C:0.52, G:0.20, T:0.09
Consensus pattern (13 bp):
GACCCGACTGCCC
Found at i:1294032 original size:35 final size:35
Alignment explanation
Indices: 1293954--1294068 Score: 144
Period size: 35 Copynumber: 3.3 Consensus size: 35
1293944 AAAGTTTGCA
* *
1293954 TCGATTCAAGTCGAACA-GAAGGAAGCATGAGAACTT
1 TCGATTCAAGTCGAA-AGGAAGGAAGCAT-CGCACTT
*
1293990 TCGATTCAAGTCGAAAGGAAGGAAGTATCGCACTT
1 TCGATTCAAGTCGAAAGGAAGGAAGCATCGCACTT
*
1294025 TCGATTCAAGTC-AAACGGAAGGAGGCATCGCACTT
1 TCGATTCAAGTCGAAA-GGAAGGAAGCATCGCACTT
*
1294060 TCCATTCAA
1 TCGATTCAA
1294069 CTAGAACGGA
Statistics
Matches: 71, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
34 3 0.04
35 43 0.61
36 25 0.35
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (35 bp):
TCGATTCAAGTCGAAAGGAAGGAAGCATCGCACTT
Found at i:1302223 original size:9 final size:8
Alignment explanation
Indices: 1302195--1302306 Score: 56
Period size: 8 Copynumber: 13.5 Consensus size: 8
1302185 AAATTTTTGG
1302195 AAAA-AAT
1 AAAATAAT
1302202 AATAA-AAT
1 AA-AATAAT
1302210 AAAATAAT
1 AAAATAAT
1302218 AGAAATAAT
1 A-AAATAAT
*
1302227 AATACTAAT
1 AA-AATAAT
1302236 AAAATATAAT
1 -AAA-ATAAT
1302246 AAAAT-AT
1 AAAATAAT
*
1302253 AAAAGAAAT
1 AAAA-TAAT
1302262 GAAAAATAA-
1 --AAAATAAT
1302271 ATAAATAA-
1 A-AAATAAT
**
1302279 AAAAGTAGG
1 AAAA-TAAT
1302288 AAAATAA-
1 AAAATAAT
1302295 AAAATAAT
1 AAAATAAT
1302303 AAAA
1 AAAA
1302307 AAGGTTAGAC
Statistics
Matches: 85, Mismatches: 6, Indels: 27
0.72 0.05 0.23
Matches are distributed among these distances:
7 21 0.25
8 29 0.34
9 23 0.27
10 8 0.09
11 4 0.05
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (8 bp):
AAAATAAT
Found at i:1302270 original size:26 final size:26
Alignment explanation
Indices: 1302206--1302283 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 26
1302196 AAAAATAATA
* *
1302206 AAAT-AAAATAATAGAAATAATAATAC
1 AAATAAAAATAATAGAAAT-ATAAAAG
*
1302232 TAATAAAATATAATA-AAATATAAAAG
1 AAATAAAA-ATAATAGAAATATAAAAG
* *
1302258 AAATGAAAAATAA-ATAAATAAAAAAG
1 AAAT-AAAAATAATAGAAATATAAAAG
1302284 TAGGAAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
25 1 0.02
26 25 0.58
27 11 0.26
28 6 0.14
ACGTcount: A:0.72, C:0.01, G:0.05, T:0.22
Consensus pattern (26 bp):
AAATAAAAATAATAGAAATATAAAAG
Found at i:1302307 original size:16 final size:16
Alignment explanation
Indices: 1302195--1302307 Score: 65
Period size: 16 Copynumber: 6.9 Consensus size: 16
1302185 AAATTTTTGG
1302195 AAAAAATAAT-AAAAT
1 AAAAAATAATAAAAAT
*
1302210 --AAAATAATAGAAAT
1 AAAAAATAATAAAAAT
*
1302224 AATAATACTAATAAAATAT
1 AA-AA-AATAATAAAA-AT
*
1302243 AATAAAATATAAAAGAAAT
1 AA-AAAATA-ATAA-AAAT
* *
1302262 GAAAAATAA-ATAAAT
1 AAAAAATAATAAAAAT
**
1302277 AAAAAAGT-AGGAAAAT
1 AAAAAA-TAATAAAAAT
1302293 AAAAAATAATAAAAA
1 AAAAAATAATAAAAA
1302308 AGGTTAGACT
Statistics
Matches: 75, Mismatches: 12, Indels: 21
0.69 0.11 0.19
Matches are distributed among these distances:
13 8 0.11
14 4 0.05
15 11 0.15
16 17 0.23
17 3 0.04
18 17 0.23
19 13 0.17
20 2 0.03
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.20
Consensus pattern (16 bp):
AAAAAATAATAAAAAT
Found at i:1304445 original size:85 final size:85
Alignment explanation
Indices: 1304310--1305179 Score: 892
Period size: 85 Copynumber: 10.2 Consensus size: 85
1304300 AGCTAAATGG
* * * * ** * * * **
1304310 AATCAAACTCGAAGGTATTTGTTGACATATAGCTTTTCTCGA-CTTAAGCTATGCTATGAATTTT
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTC-ACCTTGAGCTATGCTGTAAATTGG
* ** *
1304374 ACATGCCCCTGAGCTGAATGT
65 ATATGCCTTTGAGCTGAGTGT
* * ** *
1304395 AATAGAACTCGAAGGTCTTTGTTGATAGATAACCCTTCTTGCTTTGAGCTATGCTGTAAATTGGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTGGA
*
1304460 TATGCCTTTGAGCTGAGTCT
66 TATGCCTTTGAGCTGAGTGT
* ** *
1304480 AATTGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTTTCCTTGAGTTATGCTGTAAATTGG
1 AATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTGG
* *
1304545 ATGTGCCTTTGAGCTGAGTCT
65 ATATGCCTTTGAGCTGAGTGT
* * * * *
1304566 AATCAAACTTGAAGGT-TTTGGTTGACAGATAACCCTTCTCACCTTAAGTTATGATGTAAATTGG
1 AATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTGG
*
1304630 ATGTGCCTTTGAGCTGAGTGT
65 ATATGCCTTTGAGCTGAGTGT
* * * ** *
1304651 AATCGAACTCGAAGGTCTTTTGTTGAAATATAGCCCTTCTCGTCTTGAGCTATGCTGTAAATTTG
1 AATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTGG
*
1304716 ATATGCCTTCGAGCTGAGTGT
65 ATATGCCTTTGAGCTGAGTGT
* * * * * * ** *
1304737 AATCGAGCTCGAAGGTCTTGGTTAACAGATAACCCTTTTCCCCTTGAGTTATATTGT--ACTGGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTGGA
* *
1304800 TACGCCTTTGAGCTGAATGT
66 TATGCCTTTGAGCTGAGTGT
* * * ** *
1304820 AATCGAACTCGAAGGTCTTTTGTTGAAAGATAGCCCTTCTCACCTTGATCTATGCTAAAAATTTG
1 AATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTGG
*
1304885 A-ATTGCCTCTGAGCTGAGTGT
65 ATA-TGCCTTTGAGCTGAGTGT
* * *
1304906 AATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCACCTTGAGTTATGTTGT--ATTGGA
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTGGA
* *
1304969 TATGTCTTTGAGCTGAATGT
66 TATGCCTTTGAGCTGAGTGT
* * * * *
1304989 AATCGAACTCGAAGGTATTTTGTTAACAGATAGCCCTTCTCACCTTCAGCTATGCTGTAAATTTG
1 AATCGAACTCGAAGGT-CTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTGG
* * *
1305054 ATTTGCCTCTGAGCTGAGAGT
65 ATATGCCTTTGAGCTGAGTGT
* * * * * *
1305075 AATTGAACTCAAAGGTCTTGGTTGACAGATAACCCTTCTCGCCTTGAGCTATACTATAAATTTGG
1 AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAA-TTGG
* *
1305140 -TATGCCTCTAAGCTGAGTGT
65 ATATGCCTTTGAGCTGAGTGT
*
1305160 AATCAAACTCGAAGGTCTTT
1 AATCGAACTCGAAGGTCTTT
1305180 ATTGGTAGAT
Statistics
Matches: 645, Mismatches: 126, Indels: 28
0.81 0.16 0.04
Matches are distributed among these distances:
83 73 0.11
84 66 0.10
85 284 0.44
86 219 0.34
87 3 0.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.35
Consensus pattern (85 bp):
AATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGTAAATTGGA
TATGCCTTTGAGCTGAGTGT
Found at i:1304847 original size:169 final size:170
Alignment explanation
Indices: 1304299--1305179 Score: 988
Period size: 169 Copynumber: 5.2 Consensus size: 170
1304289 ATGTGTCATC
* * * * * * ** *
1304299 GAGCTAAATGGAATCAAACTCGAAGGT-ATTTGTTGACATATAGCTTTTCTCGA-CTTAAGCTAT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAGATAGCCCTTCTC-ACCTTGAGCTAT
* * * * * * * * *
1304362 GCTATGAATTTTACATGCCCCTGAGCTGAATGTAATAGAACTCGAAGGTCTTTGTTGATAGATAA
65 GCTGTAAATTTGATATGCCTCTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAA
** * * **
1304427 CCCTTCTTGCTTTGAGCTATGCTGTAAATTGGATATGCCTTT
130 CCCTTCTCACCTTGAGTTATATTGT-AATTGGATATGCCTTT
* * * * * ** *
1304469 GAGCTGAGTCTAATTGAACTCGAAGGTCTTTTGTTGACAGATAACCCTTCTTTCCTTGAGTTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAGATAGCCCTTCTCACCTTGAGCTATG
* * * * * * *
1304534 CTGTAAATTGGATGTGCCTTTGAGCTGAGTCTAATCAAACTTGAAGGTTTTGGTTGACAGATAAC
66 CTGTAAATTTGATATGCCTCTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
* *
1304599 CCTTCTCACCTTAAGTTATGA-TGTAAATTGGATGTGCCTTT
131 CCTTCTCACCTTGAGTTAT-ATTGT-AATTGGATATGCCTTT
* * **
1304640 GAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGTTGAAATATAGCCCTTCTCGTCTTGAGCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAGATAGCCCTTCTCACCTTGAGCTATG
* *
1304705 CTGTAAATTTGATATGCCT-TCGAGCTGAGTGTAATCGAGCTCGAAGGTCTTGGTTAACAGATAA
66 CTGTAAATTTGATATGCCTCT-GAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAA
* * * *
1304769 CCCTTTTCCCCTTGAGTTATATTGT-ACTGGATACGCCTTT
130 CCCTTCTCACCTTGAGTTATATTGTAATTGGATATGCCTTT
*
1304809 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAGATAGCCCTTCTCACCTTGATCTATG
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAGATAGCCCTTCTCACCTTGAGCTATG
**
1304874 CTAAAAATTTGA-ATTGCCTCTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAA
66 CTGTAAATTTGATA-TGCCTCTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAA
* *
1304938 CCCTTCTCACCTTGAGTTATGTTGT-ATTGGATATGTCTTT
130 CCCTTCTCACCTTGAGTTATATTGTAATTGGATATGCCTTT
* *
1304978 GAGCTGAATGTAATCGAACTCGAAGGTATTTTGTT-AACAGATAGCCCTTCTCACCTTCAGCTAT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAA-AGATAGCCCTTCTCACCTTGAGCTAT
* * * *
1305042 GCTGTAAATTTGATTTGCCTCTGAGCTGAGAGTAATTGAACTCAAAGGTCTTGGTTGACAGATAA
65 GCTGTAAATTTGATATGCCTCTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAA
* * * * *
1305107 CCCTTCTCGCCTTGAGCTATACTATAAATTTGG-TATGCCTCT
130 CCCTTCTCACCTTGAGTTATATTGT-AA-TTGGATATGCCTTT
* * *
1305149 AAGCTGAGTGTAATCAAACTCGAAGGTCTTT
1 GAGCTGAATGTAATCGAACTCGAAGGTCTTT
1305180 ATTGGTAGAT
Statistics
Matches: 603, Mismatches: 96, Indels: 23
0.84 0.13 0.03
Matches are distributed among these distances:
168 3 0.00
169 298 0.49
170 24 0.04
171 274 0.45
172 4 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (170 bp):
GAGCTGAATGTAATCGAACTCGAAGGTCTTTTGTTGAAAGATAGCCCTTCTCACCTTGAGCTATG
CTGTAAATTTGATATGCCTCTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAAC
CCTTCTCACCTTGAGTTATATTGTAATTGGATATGCCTTT
Found at i:1317957 original size:11 final size:11
Alignment explanation
Indices: 1317943--1317967 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1317933 AATATAAAAT
1317943 AATTAATTATA
1 AATTAATTATA
1317954 AATTAATTATA
1 AATTAATTATA
1317965 AAT
1 AAT
1317968 AAGAAAGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTAATTATA
Found at i:1320136 original size:17 final size:17
Alignment explanation
Indices: 1320098--1320138 Score: 75
Period size: 16 Copynumber: 2.5 Consensus size: 17
1320088 GGTTACCATG
1320098 ACATTTTTTGGCCTAGA
1 ACATTTTTTGGCCTAGA
1320115 A-ATTTTTTGGCCTAGA
1 ACATTTTTTGGCCTAGA
1320131 ACATTTTT
1 ACATTTTT
1320139 CCCAGTTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 16 0.70
17 7 0.30
ACGTcount: A:0.24, C:0.15, G:0.15, T:0.46
Consensus pattern (17 bp):
ACATTTTTTGGCCTAGA
Found at i:1324951 original size:20 final size:20
Alignment explanation
Indices: 1324923--1324961 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
1324913 ATATACTACG
1324923 TAGTATATAT-AACTATATAA
1 TAGTATATATGAAC-ATATAA
*
1324943 TAGTGTATATGAACATATA
1 TAGTATATATGAACATATA
1324962 GTATACTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.38
Consensus pattern (20 bp):
TAGTATATATGAACATATAA
Found at i:1325968 original size:85 final size:85
Alignment explanation
Indices: 1325707--1326514 Score: 847
Period size: 86 Copynumber: 9.5 Consensus size: 85
1325697 GAATTTTACT
* * * * * ** *
1325707 TGCCCTTGAACTGAATGTAATGGAACTCGAAGGTCTTTGTTGACATATGGGCCCTTCTTACCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGAT-AACCCTTCTCACCTTG
1325772 AGCTATGCTGTAAATTGGATA
65 AGCTATGCTGTAAATTGGATA
* * * * * **
1325793 TGCCTTTGAGCTGAGTATAATCAAACTCGAAGGTCTTTTGTTGATAGATAGCCCTTATTTCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCACCTTG
* * *
1325858 AGTTATACTGTAAATTGGATG
65 AGCTATGCTGTAAATTGGATA
* * * * *
1325879 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACATATCACCCTTCTCGCCTTAA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGA
* *
1325944 GTTATGCTGTAAATTGGATG
66 GCTATGCTGTAAATTGGATA
* * * * **
1325964 TGCCTTTGAGCTGATTGTAATCAAACTCGAAGGTCTTTTGATGACATATAACCCTTCTCGTCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCACCTTG
* *
1326029 AGCTATGTTGTAAATTTGATA
65 AGCTATGCTGTAAATTGGATA
* * * *
1326050 TGCCTTTAAACTGAGTGTAATCGAACTCGAAGGT-TTTGGTTGACAGATAACCCTTTTCCCCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTT-GTTGACAGATAACCCTTCTCACCTTG
* * *
1326114 AGTTATGTTGT--ATTAGATA
65 AGCTATGCTGTAAATTGGATA
* * * * *
1326133 TGCCTTTGAGTTGAATGTAATCGAACTCGAAGGACTTTTGTTGACAGATAGCCCTTTTCACCTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCACCTTG
* *
1326198 AGCTATGCTATAAACTT-GATT
65 AGCTATGCTGTAAA-TTGGATA
* * * *
1326219 TGTCTCTGAGCTGAGTGTAATCGAACTCAAAGGTCTTGGTTGACAGATAACCCTTCTCACCTTGA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGA
* * *
1326284 GTTATGTTGT--ACTGGATA
66 GCTATGCTGTAAATTGGATA
* * * * * * *
1326302 TGTCTTTAAGCTGAATGTAATCGAACTCAAAGGTCTTTTGTTGACAGATAGCCCTTCTCTCCTTC
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTC-TTTGTTGACAGATAACCCTTCTCACCTTG
* *
1326367 AGCTATGCTGTAAATTTGATT
65 AGCTATGCTGTAAATTGGATA
* * * *
1326388 TGCCTCTGAGCTGAGTGTAATTGAACTCGAAGGTCCTCGTTGACAGATAACCCTTCTCACCTTGA
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGA
1326453 GCTATGCTGTAAATTTGG-TA
66 GCTATGCTGTAAA-TTGGATA
* * * * *
1326473 TGCCTCTAAGATGAGTGTAACCGAACTCAAAGGTCTTTGTTG
1 TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTG
1326515 GTATATGCTT
Statistics
Matches: 604, Mismatches: 105, Indels: 27
0.82 0.14 0.04
Matches are distributed among these distances:
82 1 0.00
83 72 0.12
84 69 0.11
85 215 0.36
86 234 0.39
87 13 0.02
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (85 bp):
TGCCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCACCTTGA
GCTATGCTGTAAATTGGATA
Found at i:1326235 original size:169 final size:169
Alignment explanation
Indices: 1325717--1326463 Score: 920
Period size: 169 Copynumber: 4.4 Consensus size: 169
1325707 TGCCCTTGAA
* * * * ** * *
1325717 CTGAATGTAATGGAACTCGAAGGTCTTTGTTGACATATGGGCCCTTCTTACCTTGAGCTATGCTG
1 CTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGAT-AACCCTTCTCACCTTGAGTTATGCTG
* * *
1325782 TAAATTGGATATGCCTTTGAGCTGAGTATAATCAAACTCGAAGGTCTTTTGTTGATAGATAGCCC
65 T--ATTGGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCC
* * * * * * *
1325847 TTATTTCCTTGAGTTATACTGTAAATTGGATGTGCCTTTGAG
128 TTCTCTCCTTGAGCTATGCTGTAAATTTGATTTGCCTCTGAG
* * * *
1325889 CTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACATATCACCCTTCTCGCCTTAAGTTATGCTGT
1 CTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGT
* * * * *
1325954 AAATTGGATGTGCCTTTGAGCTGATTGTAATCAAACTCGAAGGTCTTTTGATGACATATAACCCT
66 --ATTGGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCT
* * * * *
1326019 TCTCGT-CTTGAGCTATGTTGTAAATTTGATATGCCTTTAAA
129 TCTC-TCCTTGAGCTATGCTGTAAATTTGATTTGCCTCTGAG
* * * *
1326060 CTGAGTGTAATCGAACTCGAAGGTTTTGGTTGACAGATAACCCTTTTCCCCTTGAGTTATGTTGT
1 CTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGT
* * * * *
1326125 ATTAGATATGCCTTTGAGTTGAATGTAATCGAACTCGAAGGACTTTTGTTGACAGATAGCCCTTT
66 ATTGGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTC
* * * *
1326190 TCACCTTGAGCTATGCTATAAACTTGATTTGTCTCTGAG
131 TCTCCTTGAGCTATGCTGTAAATTTGATTTGCCTCTGAG
* *
1326229 CTGAGTGTAATCGAACTCAAAGGTCTTGGTTGACAGATAACCCTTCTCACCTTGAGTTATGTTGT
1 CTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGT
* * * * *
1326294 ACTGGATATGTCTTTAAGCTGAATGTAATCGAACTCAAAGGTCTTTTGTTGACAGATAGCCCTTC
66 ATTGGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTC
*
1326359 TCTCCTTCAGCTATGCTGTAAATTTGATTTGCCTCTGAG
131 TCTCCTTGAGCTATGCTGTAAATTTGATTTGCCTCTGAG
* * * *
1326398 CTGAGTGTAATTGAACTCGAAGGTCCTCGTTGACAGATAACCCTTCTCACCTTGAGCTATGCTGT
1 CTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGT
1326463 A
66 A
1326464 AATTTGGTAT
Statistics
Matches: 499, Mismatches: 74, Indels: 7
0.86 0.13 0.01
Matches are distributed among these distances:
169 296 0.59
171 167 0.33
172 36 0.07
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (169 bp):
CTGAGTGTAATCGAACTCGAAGGTCTTGGTTGACAGATAACCCTTCTCACCTTGAGTTATGCTGT
ATTGGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTTGTTGACAGATAGCCCTTC
TCTCCTTGAGCTATGCTGTAAATTTGATTTGCCTCTGAG
Found at i:1332327 original size:21 final size:21
Alignment explanation
Indices: 1332302--1332381 Score: 83
Period size: 21 Copynumber: 3.8 Consensus size: 21
1332292 CAGAACCCCA
*
1332302 GGGGGTATCGATTCCCCT-AT
1 GGGGGAATCGATTCCCCTCAT
* *
1332322 GGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATTCCCC-TC-AT
1332346 GGGGGAATCGATT-CCCTCAT
1 GGGGGAATCGATTCCCCTCAT
*
1332366 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
1332382 TCTGCACTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
20 13 0.27
21 19 0.39
22 4 0.08
23 12 0.24
24 1 0.02
ACGTcount: A:0.17, C:0.25, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTCAT
Found at i:1332375 original size:20 final size:21
Alignment explanation
Indices: 1332302--1332383 Score: 78
Period size: 20 Copynumber: 3.9 Consensus size: 21
1332292 CAGAACCCCA
* *
1332302 GGGGGTATCGATTCCC-CTAT
1 GGGGGAATCGATTCCCTCAAT
* *
1332322 GGGGGGAATCGGTTCCCCTTCAAA
1 -GGGGGAATCGATT-CCC-TCAAT
1332346 GGGGGAATCGATTCCCTC-AT
1 GGGGGAATCGATTCCCTCAAT
*
1332366 GGGGGTATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
1332384 TGCACTAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 18 0.35
21 13 0.25
22 6 0.12
23 12 0.24
24 2 0.04
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAT
Found at i:1336197 original size:22 final size:21
Alignment explanation
Indices: 1336155--1336194 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1336145 GAGTTTATTT
*
1336155 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1336176 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1336195 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1340269 original size:30 final size:30
Alignment explanation
Indices: 1340179--1340269 Score: 110
Period size: 30 Copynumber: 2.9 Consensus size: 30
1340169 AAAATTTATC
* *
1340179 AAACTAACAAACTAATTTTTTTAAATATAACTT
1 AAACTAATAAACT-A-TTTTTT-AATATAATTT
* * *
1340212 AAATTAATCAACTGTTTTTTAATATAATTT
1 AAACTAATAAACTATTTTTTAATATAATTT
1340242 AAACTAATAAACTATTTTTTAATATAAT
1 AAACTAATAAACTATTTTTTAATATAAT
1340270 ATAACTTAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
30 34 0.68
31 6 0.12
33 10 0.20
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (30 bp):
AAACTAATAAACTATTTTTTAATATAATTT
Found at i:1340332 original size:65 final size:66
Alignment explanation
Indices: 1340242--1340439 Score: 229
Period size: 65 Copynumber: 2.9 Consensus size: 66
1340232 AATATAATTT
* *
1340242 AAACTAATAAACTATTTTTTAATATAATATAACTTAAACTAACAAACTAATATAACT-TAAACTA
1 AAACTAATTAACTAATTTTT-ATATAATATAACTTAAACTAACAAACTAATATAACTATAAACTA
1340306 AC
65 AC
* **
1340308 AAACGAATTAACTAATTTTTATATAATATAACTTAAAGAAACAAACTAATATAACTTAATCAAAT
1 AAACTAATTAACTAATTTTTATATAATATAACTTAAACTAACAAACTAATATAAC----T---AT
1340373 AAACTAAC
59 AAACTAAC
*
1340381 AAATTAATTAACTAATTTTGTATATATAATATAACTTAAACTAACAAACTAAT-TAACTA
1 AAACTAATTAACTAA-TTT-T-TATATAATATAACTTAAACTAACAAACTAATATAACTA
1340440 ATTTTTTTAT
Statistics
Matches: 112, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
65 33 0.29
66 17 0.15
68 1 0.01
69 1 0.01
71 1 0.01
73 22 0.20
74 3 0.03
75 5 0.04
76 29 0.26
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (66 bp):
AAACTAATTAACTAATTTTTATATAATATAACTTAAACTAACAAACTAATATAACTATAAACTAA
C
Found at i:1340336 original size:42 final size:42
Alignment explanation
Indices: 1340289--1340843 Score: 258
Period size: 42 Copynumber: 12.7 Consensus size: 42
1340279 ACTAACAAAC
*
1340289 TAATATAACTTAAACTAACAAACGAATTAACTAATTTTTATA
1 TAATATAACTTAAACTAACAAACTAATTAACTAATTTTTATA
** * *
1340331 TAATATAACTTAAAGAAACAAACTAATATAACTTAA---TCAAA
1 TAATATAACTTAAACTAACAAACTAAT-TAAC-TAATTTTTATA
* ** * *
1340372 TAA-ACTAAC--AAATTAATTAACTAATT---T--TGTATATA
1 TAATA-TAACTTAAACTAACAAACTAATTAACTAATTTTTATA
1340407 TAATATAACTTAAACTAACAAACTAATTAACTAATTTTTTTATATA
1 TAATATAACTTAAACTAACAAACTAATTAACTAA---TTTT-TATA
*
1340453 TAATATAACTTAAACTAACAAATTAATTAACT-ATTTTTCATA
1 TAATATAACTTAAACTAACAAACTAATTAACTAATTTTT-ATA
* * *
1340495 TAATATAACTTAAACTAACAAACT-ACT-A-TAA-TATAACT-
1 TAATATAACTTAAACTAACAAACTAATTAACTAATTTTTA-TA
*
1340533 TAA-ACTAAC--AAACTAACAAACTAATTAATTAATTTTTTTATA
1 TAATA-TAACTTAAACTAACAAACTAATTAACTAA--TTTTTATA
* * *** *
1340575 TAATATAACATAAACTAACAAACTAATATAACTTAAACTAACAAA
1 TAATATAACTTAAACTAACAAACTAAT-TAAC-T-AATTTTTATA
* * ** * * *
1340620 CTAAT-TAACTACTTTTTTTATA-TAATATAACTTAAACAAACAAACTATTATA
1 -TAATAT-A--AC-----TTAAACTAACA-AAC-T-AATTAACTAATTTTTATA
*
1340672 -ACT-TAAACTAATAAACTAACAAACTAATTAACTAATTTTTTTATATA
1 TAATAT-AACT--TAAACTAACAAACTAATTAACTAA---TTTT-TATA
1340719 TAATATAACTTAAACTAACAAACTAACAAATTAATTAACTAATTTTTATATA
1 TAATATAACTTAAACTAAC--A--AAC----TAATTAACTAA-TTTT-TATA
1340771 TAATATAACTTAAACTAACAAACTAATTAACTAGATTTTTTTATA
1 TAATATAACTTAAACTAACAAACTAATTAACTA-A--TTTTTATA
1340816 TAATATAACTTAAACTAACAAACTAATT
1 TAATATAACTTAAACTAACAAACTAATT
1340844 TAAACATTAA
Statistics
Matches: 398, Mismatches: 49, Indels: 129
0.69 0.09 0.22
Matches are distributed among these distances:
34 1 0.00
35 9 0.02
36 14 0.04
37 17 0.04
38 10 0.03
39 19 0.05
40 4 0.01
41 14 0.04
42 64 0.16
43 13 0.03
44 30 0.08
45 49 0.12
46 61 0.15
47 6 0.02
48 14 0.04
49 1 0.00
50 9 0.02
52 40 0.10
53 6 0.02
54 15 0.04
55 2 0.01
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.36
Consensus pattern (42 bp):
TAATATAACTTAAACTAACAAACTAATTAACTAATTTTTATA
Found at i:1340379 original size:23 final size:23
Alignment explanation
Indices: 1340266--1340366 Score: 102
Period size: 23 Copynumber: 4.6 Consensus size: 23
1340256 TTTTTTAATA
1340266 TAATATAACTTAAACTAACAAAC
1 TAATATAACTTAAACTAACAAAC
1340289 TAATATAACTTAAACTAACAAAC
1 TAATATAACTTAAACTAACAAAC
* * *** *
1340312 GAAT-TAAC-T-AATTTTTATA-
1 TAATATAACTTAAACTAACAAAC
**
1340331 TAATATAACTTAAAGAAACAAAC
1 TAATATAACTTAAACTAACAAAC
1340354 TAATATAACTTAA
1 TAATATAACTTAA
1340367 TCAAATAAAC
Statistics
Matches: 61, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
19 3 0.05
20 9 0.15
21 2 0.03
22 8 0.13
23 39 0.64
ACGTcount: A:0.54, C:0.13, G:0.02, T:0.31
Consensus pattern (23 bp):
TAATATAACTTAAACTAACAAAC
Found at i:1340411 original size:53 final size:50
Alignment explanation
Indices: 1340354--1340507 Score: 145
Period size: 46 Copynumber: 3.3 Consensus size: 50
1340344 AGAAACAAAC
*
1340354 TAATATAACTTAATCAAATAAACTAACAAATTAATTAACTAA-TTTTGTATATA
1 TAATATAACTTAAT----TAAACTAACAAACTAATTAACTAATTTTTGTATATA
*
1340407 TAATATAAC----TTAAACTAACAAACTAATTAACTAATTTTTTTATATA
1 TAATATAACTTAATTAAACTAACAAACTAATTAACTAATTTTTGTATATA
* *
1340453 TAATATAAC----TTAAACTAACAAATTAATTAACT-A-TTTT-T-CATA
1 TAATATAACTTAATTAAACTAACAAACTAATTAACTAATTTTTGTATATA
1340495 TAATATAACTTAA
1 TAATATAACTTAA
1340508 ACTAACAAAC
Statistics
Matches: 92, Mismatches: 4, Indels: 17
0.81 0.04 0.15
Matches are distributed among these distances:
42 12 0.13
43 1 0.01
44 4 0.04
45 24 0.26
46 41 0.45
49 1 0.01
53 9 0.10
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (50 bp):
TAATATAACTTAATTAAACTAACAAACTAATTAACTAATTTTTGTATATA
Found at i:1340470 original size:164 final size:167
Alignment explanation
Indices: 1340289--1340607 Score: 468
Period size: 164 Copynumber: 1.9 Consensus size: 167
1340279 ACTAACAAAC
*
1340289 TAATATAACTTAAACTAACAAACGAATTAACTAATTTTT-ATATAATATAACTTAAAGAAAC-AA
1 TAATATAACTTAAACTAACAAACGAATTAACT-ATTTTTCATATAATATAACTTAAACAAACAAA
* * *
1340352 -AC-TAATATAACTTAATCAAATAAACTAACAAATTAATTAACTAATTTTGTATATATAATATAA
65 CACATAATATAACTTAAACAAACAAACTAACAAACTAATTAACTAATTTT-TATATATAATATAA
*
1340415 CTTAAACTAACAAACTAAT-TAACTAATTTTTTTATATA
129 CATAAACTAACAAACTAATATAACTAATTTTTTTATATA
** *
1340453 TAATATAACTTAAACTAACAAATTAATTAACTATTTTTCATATAATATAACTTAAACTAACAAAC
1 TAATATAACTTAAACTAACAAACGAATTAACTATTTTTCATATAATATAACTTAAACAAACAAAC
* * *
1340518 TACTATAATATAACTTAAACTAACAAACTAACAAACTAATTAATTAATTTTTTTATATAATATAA
66 -AC-ATAATATAACTTAAACAAACAAACTAACAAACTAATTAACTAATTTTTATATATAATATAA
1340583 CATAAACTAACAAACTAATATAACT
129 CATAAACTAACAAACTAATATAACT
1340608 TAAACTAACA
Statistics
Matches: 137, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
163 6 0.04
164 50 0.36
165 2 0.01
167 2 0.01
168 31 0.23
169 46 0.34
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.35
Consensus pattern (167 bp):
TAATATAACTTAAACTAACAAACGAATTAACTATTTTTCATATAATATAACTTAAACAAACAAAC
ACATAATATAACTTAAACAAACAAACTAACAAACTAATTAACTAATTTTTATATATAATATAACA
TAAACTAACAAACTAATATAACTAATTTTTTTATATA
Found at i:1340525 original size:28 final size:28
Alignment explanation
Indices: 1340493--1340547 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1340483 CTATTTTTCA
1340493 TATAATATAACTTAAACTAACAAACTAC
1 TATAATATAACTTAAACTAACAAACTAC
1340521 TATAATATAACTTAAACTAACAAACTA
1 TATAATATAACTTAAACTAACAAACTA
1340548 ACAAACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.55, C:0.16, G:0.00, T:0.29
Consensus pattern (28 bp):
TATAATATAACTTAAACTAACAAACTAC
Found at i:1340530 original size:75 final size:76
Alignment explanation
Indices: 1340453--1340758 Score: 324
Period size: 67 Copynumber: 4.1 Consensus size: 76
1340443 TTTTTATATA
* *
1340453 TAATATAACTTAAACTAACAAATTAATTAACT-A-TTTTTCATATAATATAACTTAAACTAACAA
1 TAATATAACTTAAACTAACAAACTAATTAACTAATTTTTTTATATAATATAACTTAAACTAACAA
1340516 ACTACTATAAT
66 ACTACTATAAT
* * *
1340527 ATAACT-TAAACTAACAAACTAACAAACTAATTAATTAATTTTTTTATATAATATAACATAAACT
1 -TAA-TAT-AACT--TAAACTAACAAACTAATTAACTAATTTTTTTATATAATATAACTTAAACT
1340591 AAC-AA--AC------
61 AACAAACTACTATAAT
* *
1340598 TAATATAACTTAAACTAACAAACTAATTAACTACTTTTTTTATATAATATAACTTAAACAAACAA
1 TAATATAACTTAAACTAACAAACTAATTAACTAATTTTTTTATATAATATAACTTAAACTAACAA
*
1340663 ACTATTATAACT
66 ACTACTATAA-T
1340675 TAA-ACTAA--TAAACTAACAAACTAATTAACTAATTTTTTTATATATAATATAACTTAAACTAA
1 TAATA-TAACTTAAACTAACAAACTAATTAACTAA-TTTTTT-TATATAATATAACTTAAACTAA
1340737 CAAACTAAC-A-AAT
63 CAAACT-ACTATAAT
1340750 TAAT-TAACT
1 TAATATAACT
1340759 AATTTTTATA
Statistics
Matches: 193, Mismatches: 14, Indels: 47
0.76 0.06 0.19
Matches are distributed among these distances:
67 48 0.25
68 2 0.01
69 5 0.03
70 5 0.03
74 3 0.02
75 31 0.16
76 14 0.07
77 36 0.19
78 20 0.10
79 3 0.02
80 26 0.13
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (76 bp):
TAATATAACTTAAACTAACAAACTAATTAACTAATTTTTTTATATAATATAACTTAAACTAACAA
ACTACTATAAT
Found at i:1340605 original size:23 final size:23
Alignment explanation
Indices: 1340575--1340628 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
1340565 TTTTTTTATA
1340575 TAATATAACATAAACTAACAAAC
1 TAATATAACATAAACTAACAAAC
*
1340598 TAATATAACTTAAACTAACAAAC
1 TAATATAACATAAACTAACAAAC
1340621 TAAT-TAAC
1 TAATATAAC
1340629 TACTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.13
23 26 0.87
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (23 bp):
TAATATAACATAAACTAACAAAC
Found at i:1340672 original size:23 final size:23
Alignment explanation
Indices: 1340645--1340689 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1340635 TTTTATATAA
1340645 TATAACTTAAACAAACAAACTAT
1 TATAACTTAAACAAACAAACTAT
* *
1340668 TATAACTTAAACTAATAAACTA
1 TATAACTTAAACAAACAAACTA
1340690 ACAAACTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.56, C:0.16, G:0.00, T:0.29
Consensus pattern (23 bp):
TATAACTTAAACAAACAAACTAT
Found at i:1340697 original size:16 final size:16
Alignment explanation
Indices: 1340676--1340706 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1340666 ATTATAACTT
1340676 AAACTAATAAACTAAC
1 AAACTAATAAACTAAC
*
1340692 AAACTAATTAACTAA
1 AAACTAATAAACTAA
1340707 TTTTTTTATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.16, G:0.00, T:0.23
Consensus pattern (16 bp):
AAACTAATAAACTAAC
Found at i:1340712 original size:142 final size:145
Alignment explanation
Indices: 1340453--1340744 Score: 459
Period size: 142 Copynumber: 2.0 Consensus size: 145
1340443 TTTTTATATA
* *
1340453 TAATATAACTTAAACTAACAAATTAATTAACTATTTTTCATATAATATAACTTAAACTAACAAAC
1 TAATATAACTTAAACTAACAAACTAATTAACTATTTTTCATATAATATAACTTAAACAAACAAAC
*
1340518 TACTATAATATAACTTAAACTAACAAACTAACAAACTAATTAATTAA-TTTTTT-TATATAATAT
66 -ACTAT-ATATAACTTAAACTAACAAACTAACAAACTAATTAACTAATTTTTTTATATATAATAT
1340581 AACATAAACTAACAAAC
129 AACATAAACTAACAAAC
*
1340598 TAATATAACTTAAACTAACAAACTAATTAACTACTTTTTTTATATAATATAACTTAAACAAAC-A
1 TAATATAACTTAAACTAACAAACTAATTAACTA--TTTTTCATATAATATAACTTAAACAAACAA
*
1340662 A-ACTAT-TATAACTTAAACTAATAAACTAACAAACTAATTAACTAATTTTTTTATATATAATAT
64 ACACTATATATAACTTAAACTAACAAACTAACAAACTAATTAACTAATTTTTTTATATATAATAT
*
1340725 AACTTAAACTAACAAAC
129 AACATAAACTAACAAAC
1340742 TAA
1 TAA
1340745 CAAATTAATT
Statistics
Matches: 137, Mismatches: 6, Indels: 9
0.90 0.04 0.06
Matches are distributed among these distances:
142 37 0.27
143 6 0.04
144 34 0.25
145 32 0.23
146 2 0.01
147 26 0.19
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (145 bp):
TAATATAACTTAAACTAACAAACTAATTAACTATTTTTCATATAATATAACTTAAACAAACAAAC
ACTATATATAACTTAAACTAACAAACTAACAAACTAATTAACTAATTTTTTTATATATAATATAA
CATAAACTAACAAAC
Found at i:1340734 original size:54 final size:53
Alignment explanation
Indices: 1340668--1340841 Score: 242
Period size: 54 Copynumber: 3.4 Consensus size: 53
1340658 AACAAACTAT
*
1340668 TATAACTTAAACTAATAAACTAACAAACTAATTAACTAATTTTTTTATATATAA
1 TATAACTTAAACTAACAAACTAACAAACTAATTAACTAA-TTTTTTATATATAA
*
1340722 TATAACTTAAACTAACAAACTAACAAATTAATTAACTAA-TTTTTATATATAA
1 TATAACTTAAACTAACAAACTAACAAACTAATTAACTAATTTTTTATATATAA
1340774 TATAAC-T----T---AAACTAACAAACTAATTAACTAGATTTTTT-TATATAA
1 TATAACTTAAACTAACAAACTAACAAACTAATTAACTA-ATTTTTTATATATAA
1340819 TATAACTTAAACTAACAAACTAA
1 TATAACTTAAACTAACAAACTAA
1340842 TTTAAACATT
Statistics
Matches: 107, Mismatches: 3, Indels: 21
0.82 0.02 0.16
Matches are distributed among these distances:
44 21 0.20
45 14 0.13
46 6 0.06
47 1 0.01
50 1 0.01
51 1 0.01
52 19 0.18
53 7 0.07
54 37 0.35
ACGTcount: A:0.51, C:0.12, G:0.01, T:0.37
Consensus pattern (53 bp):
TATAACTTAAACTAACAAACTAACAAACTAATTAACTAATTTTTTATATATAA
Found at i:1340910 original size:15 final size:15
Alignment explanation
Indices: 1340890--1340926 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
1340880 ACACGATCTC
1340890 TTCTTCTCCCTTTCT
1 TTCTTCTCCCTTTCT
1340905 TTCTTCTCCCTTTCT
1 TTCTTCTCCCTTTCT
1340920 TTCTTCT
1 TTCTTCT
1340927 TACCCGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
TTCTTCTCCCTTTCT
Found at i:1343068 original size:8 final size:8
Alignment explanation
Indices: 1343051--1343096 Score: 58
Period size: 8 Copynumber: 5.5 Consensus size: 8
1343041 CTATTTTTTC
1343051 AAAA-AAA
1 AAAACAAA
1343058 AAAACAAAA
1 AAAAC-AAA
1343067 AAAAGGCAAA
1 AAAA--CAAA
1343077 AAAACAAA
1 AAAACAAA
1343085 AAAACAAA
1 AAAACAAA
1343093 AAAA
1 AAAA
1343097 AAGCCAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
7 4 0.11
8 16 0.46
9 7 0.20
10 7 0.20
11 1 0.03
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (8 bp):
AAAACAAA
Found at i:1343091 original size:27 final size:26
Alignment explanation
Indices: 1343051--1343107 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
1343041 CTATTTTTTC
*
1343051 AAAAAAAAAAACAAAAAAAAGGCAAA
1 AAAAAAAAAAACAAAAAAAAAGCAAA
*
1343077 AAAACAAAAAAACAAAAAAAAAGCCAA
1 AAAA-AAAAAAACAAAAAAAAAGCAAA
1343104 AAAA
1 AAAA
1343108 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAAACAAAAAAAAAGCAAA
Found at i:1343094 original size:28 final size:26
Alignment explanation
Indices: 1343051--1343107 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 26
1343041 CTATTTTTTC
*
1343051 AAAAAAAAAAACAAAAAAAAGGCAAA
1 AAAAAAAAAAACAAAAAAAAGCCAAA
1343077 AAAACAAAAAAACAAAAAAAAAGCCAAA
1 AAAA-AAAAAAAC-AAAAAAAAGCCAAA
1343105 AAA
1 AAA
1343108 GCCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 4 0.14
27 8 0.29
28 16 0.57
ACGTcount: A:0.84, C:0.11, G:0.05, T:0.00
Consensus pattern (26 bp):
AAAAAAAAAAACAAAAAAAAGCCAAA
Found at i:1349604 original size:13 final size:13
Alignment explanation
Indices: 1349576--1349613 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
1349566 CCTTTTGTGC
1349576 TTGCATTTAGCA-T
1 TTGCATTT-GCATT
*
1349589 TTGGATTTGCATT
1 TTGCATTTGCATT
1349602 TTGCATTTGCAT
1 TTGCATTTGCAT
1349614 GTATTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.18, C:0.13, G:0.18, T:0.50
Consensus pattern (13 bp):
TTGCATTTGCATT
Found at i:1353872 original size:34 final size:35
Alignment explanation
Indices: 1353791--1354167 Score: 487
Period size: 34 Copynumber: 10.9 Consensus size: 35
1353781 AGCAAAGTCG
* * *
1353791 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
* *
1353826 ATATTAAGCCTTCACAGAAGTGTAGTGAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
1353860 ATCTTAAGCCTTCACAG-AGAAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACAGAAG-AGTAGTGAAGC-AACC
* * *
1353896 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
* *
1353931 ATCTTAAGCCTTCACATAAGAGTAGTAAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
*
1353965 ATCTTAAGCCTTCACAGAGGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-AACC
* * * * *
1354001 ATCTTAATCCTTCACCGGAGAGTAGTGAAACAATC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
1354036 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
** *
1354070 ATCTTAAGCCTTCACAGGGGAGTAATGAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
* *
1354104 ATCTTAAGCTTTCACAGAGGAGTAGTGAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
*
1354138 ATCTTAAGCCTTCACCGAAGAGTAGTGAAG
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAG
1354168 TAAATCCATC
Statistics
Matches: 299, Mismatches: 37, Indels: 13
0.86 0.11 0.04
Matches are distributed among these distances:
33 2 0.01
34 149 0.50
35 87 0.29
36 59 0.20
37 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (35 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
Found at i:1353918 original size:105 final size:105
Alignment explanation
Indices: 1353791--1354167 Score: 600
Period size: 105 Copynumber: 3.6 Consensus size: 105
1353781 AGCAAAGTCG
* *
1353791 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATATTAAGCCTTCACAGAAGTGTAGTGAAG
1 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
*
1353856 CACCATCTTAAGCCTTCACAGAGAAGTAGTGAAGCAAACC
66 CACCATCTTAAGCCTTCACAGAGGAGTAGTGAAGCAAACC
* *
1353896 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACATAAGAGTAGTAAAG
1 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
1353961 CACCATCTTAAGCCTTCACAGAGGAGTAGTGAAGCAAACC
66 CACCATCTTAAGCCTTCACAGAGGAGTAGTGAAGCAAACC
* *
1354001 ATCTTAATCCTTCACCGGAGAGTAGTGAAACAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
1 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
* *
1354066 CACCATCTTAAGCCTTCACAGGGGAGTAATGAAGC--ACC
66 CACCATCTTAAGCCTTCACAGAGGAGTAGTGAAGCAAACC
* * * *
1354104 ATCTTAAGCTTTCA-CAGAGGAGTAGTGAAGC-ACCATCTTAAGCCTTCACCGAAGAGTAGTGAA
1 ATCTTAAGCCTTCACCGGA-GAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAA
1354167 G
65 G
1354168 TAAATCCATC
Statistics
Matches: 254, Mismatches: 17, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
102 34 0.13
103 26 0.10
105 194 0.76
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (105 bp):
ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
CACCATCTTAAGCCTTCACAGAGGAGTAGTGAAGCAAACC
Found at i:1354557 original size:42 final size:41
Alignment explanation
Indices: 1354493--1354594 Score: 132
Period size: 42 Copynumber: 2.5 Consensus size: 41
1354483 TTCACAATTT
* * * *
1354493 ATAAGTCCTTCGGGCCATCTGTAAGTCTTTTGAGCATGATG
1 ATAAATCCTTCGGGCCATCTGTAAGTCTTTAGAACAAGATG
* *
1354534 CTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAACAAGATG
1 -ATAAATCCTTCGGGCCATCTGTAAGTCTTTAGAACAAGATG
*
1354576 ATAAATCCTTCAGGCCATC
1 ATAAATCCTTCGGGCCATC
1354595 CATAAGACCT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
41 16 0.31
42 35 0.69
ACGTcount: A:0.26, C:0.22, G:0.20, T:0.32
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCTGTAAGTCTTTAGAACAAGATG
Found at i:1354773 original size:211 final size:214
Alignment explanation
Indices: 1354173--1355258 Score: 1559
Period size: 214 Copynumber: 5.1 Consensus size: 214
1354163 TGAAGTAAAT
* * *
1354173 CCATCCATAAGACTTTCAGGTAGGATGTTTTCACATGAATTTGAAAATG-AAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* * **
1354237 AGAAGATGAAACTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGT-CTTTT
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTT-ACAATTTATAAGTCCTTCG
*
1354301 GG--ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAACCCTTTAGAGC
130 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
1354364 AAGATGATAAGTCCTTCGGG
195 AAGATGATAAGTCCTTCGGG
* *
1354384 CCATCCATGAA-ACCTTCGGGTAGGATGTTTTCACATGAAATTGAAAATGAAAAAATGA-----T
1 CCATCCAT-AAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTT
1354443 -----GATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTCACAATTTATAAGTCCTT
65 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAA-TTT-ACAATTTATAAGTCCTT
* * *
1354503 CGGGCCATCTGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGA
128 CGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGA
* * *
1354568 ACAAGATGATAAATCCTTCAGG
193 GCAAGATGATAAGTCCTTCGGG
1354590 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
* *
1354655 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTT-C-A-TAATAAGTCCCTCGG
66 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTACAATTTATAAGTCCTTCGG
* * *
1354717 GCCATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCA
131 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
*
1354782 AGATGATAAGTCCTTTGGG
196 AGATGATAAGTCCTTCGGG
*
1354801 CCATCCATAAGACCTTCGGG-AGGGATGTTTTCAAATGAATTTGAAAATGAAAAAGTGATGTTTT
1 CCATCCATAAGACCTTCGGGTA-GGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTT
*
1354865 AAGAAGAT-GAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCCTC
65 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTT-ACAATTTATAAGTCCTTC
* * * * *
1354929 AGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCTGGTCATTTTTAAGCCTTTAGAG
129 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
1354994 CAAGATGATAAGTCCTTCGGG
194 CAAGATGATAAGTCCTTCGGG
* * *
1355015 TCATCCATAAAACCTTCGGG-AGGGATGTTTTCAAATGAATTTGAAAATG-AAAAGTGATGTTTT
1 CCATCCATAAGACCTTCGGGTA-GGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTT
* * * * *
1355078 AAGAATATGGAAGTTTTGAAAAAGAAGAATGTGATTTTCAAAATTTCACAGTTTATAAGTCCTTC
65 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTT-ACAATTTATAAGTCCTTC
* *
1355143 GGGCCATCAGTAATTCTTTCGAGCATGATGCTTAAATCCTTCGTGTCATCTGTAAGCCTTTAGAG
129 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
1355208 CAAGATGATAAGTCCTTCGGG
194 CAAGATGATAAGTCCTTCGGG
* * * *
1355229 CAATTCATAAAACCTTCGGGTATGATGTTT
1 CCATCCATAAGACCTTCGGGTAGGATGTTT
1355259 AAGAAGATGA
Statistics
Matches: 797, Mismatches: 54, Indels: 45
0.89 0.06 0.05
Matches are distributed among these distances:
202 36 0.05
203 17 0.02
204 5 0.01
205 2 0.00
206 127 0.16
207 1 0.00
210 38 0.05
211 202 0.25
212 12 0.02
213 23 0.03
214 292 0.37
215 4 0.01
216 38 0.05
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (214 bp):
CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTACAATTTATAAGTCCTTCGG
GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
AGATGATAAGTCCTTCGGG
Found at i:1355064 original size:417 final size:413
Alignment explanation
Indices: 1354173--1355656 Score: 1681
Period size: 417 Copynumber: 3.6 Consensus size: 413
1354163 TGAAGTAAAT
* * * *
1354173 CCATCCATAAGACTTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCAAATGAATTT----ATGAAAAATGATGTTTTAA
* **
1354238 GAAGATGAAACTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGT-CTTTTG
62 GAAGATGGAACTTTTGAAAACGAAGAATGCGATTTTCAAAATTT-AC-ATTTATAAGTCCTTCGG
*
1354302 G--ATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAACCCTTTAGAGCA
125 GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
*
1354365 AGATGATAAGTCCTTCGGGCCATCCATGAAACCTTCGGGTAGGATGTTTTCACATGAAATTGAAA
190 AGATGATAAGTCCTTCGGGCCATCCAT-AAACCTTCGGGTAGGATGTTTTCAAATGAAATTGAAA
* *
1354430 ATGAAAAAATGATGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTCACAATTTAT
254 ATGAAAAAATGAAGAAGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTCACAATTTAT
* * ** *
1354495 AAGTCCTTCGGGCCATCTGTAAGTCTTTTGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG
319 AAGTCCCTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAG
*
1354560 TCTTTAGAACAAGATGATAAATCCTTCAGG
384 CCTTTAGAACAAGATGATAAATCCTTCAGG
*
1354590 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCAAATGAATTT----ATG-AAAAATGATGTTTTA
* * *
1354655 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTT-CA-TAATAAGTCCCTCGGG
61 AGAAGATGGAACTTTTGAAAACGAAGAATGCGATTTTCAAAATTTACATTTATAAGTCCTTCGGG
* * *
1354718 CCATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGCAA
126 CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
* *
1354783 GATGATAAGTCCTTTGGGCCATCCATAAGACCTTCGGG-AGGGATGTTTTCAAATGAATTTGAAA
191 GATGATAAGTCCTTCGGGCCATCCATAA-ACCTTCGGGTA-GGATGTTTTCAAATGAAATTGAAA
1354847 ATGAAAAAGTGATGTTTTAAGAAGATGAATTTTTGAAAACGAAGAATGCGATTTTCAAAA-TTTC
254 ATGAAAAA---ATG----AAGAAG--GAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTC
*
1354911 ACAATTTATAAGTCCCTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCTGGTC
310 ACAATTTATAAGTCCCTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTC
* * * * *
1354976 ATTTTTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGG
375 ATCTGTAAGCCTTTAGAACAAGATGATAAATCCTTCAGG
* *
1355015 TCATCCATAAAACCTTCGGG-AGGGATGTTTTCAAATGAATTTGAAAATGAAAAGTGATGTTTTA
1 CCATCCATAAAACCTTCGGGTA-GGATGTTTTCAAATGAATTT----ATGAAAAATGATGTTTTA
* * * *
1355079 AGAATATGGAAGTTTTGAAAAAGAAGAATGTGATTTTCAAAATTTCACAGTTTATAAGTCCTTCG
61 AGAAGATGGAACTTTTGAAAACGAAGAATGCGATTTTCAAAATTT-ACA-TTTATAAGTCCTTCG
* *
1355144 GGCCATCAGTAATTCTTTCGAGCATGATGCTTAAATCCTTCGTGTCATCTGTAAGCCTTTAGAGC
124 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* * *
1355209 AAGATGATAAGTCCTTCGGGCAATTCATAAAACCTTCGGGTATGATG-TTT--AA-G-AA--G--
189 AAGATGATAAGTCCTTCGGGCCATCCAT-AAACCTTCGGGTAGGATGTTTTCAAATGAAATTGAA
*** * * * ** *
1355265 -ATGAAATTTTTGAA-AACGAA-----G--AATG-CG-AT----TTTCAAAAT--TTCACAATTT
253 AATGAAA-AAATGAAGAAGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTCACAATTT
* * * * * *
1355313 ATAAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTAATCTGTA
317 ATAAGTCCCTCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTA
** * * *
1355378 AGCCTTTAGAGTAAGATGATAAGTCTTTCGGG
382 AGCCTTTAGAACAAGATGATAAATCCTTCAGG
* *
1355410 CCATCCATAAAACCTTCGGGTAGGATATTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCAAATGAATTT----ATG-AAAAATGATGTTTTA
*
1355475 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
61 AGAAGATGGAACTTTTGAAAACGAAGAATGCGATTTTCAAAATTT-AC-ATTTATAAGTCCTTCG
* * *
1355540 GGCCATCAGTAAGTCTTTCGAGCACT-ATGCTTAAAATCCTTCGGGTCATTTGTGAGTCTCTT-G
124 GGCCATCAGTAAGTCTTTCGAGCA-TGATGCTT-AAATCCTTCGGGTCATCTGTAAGCCT-TTAG
* * *
1355603 AGCAAGATGATAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAGGATGTTTT
186 AGCAAGATGATAAGTCCTTCGGGCCATCCATAA-ACCTTCGGGTAGGATGTTTT
1355657 GCACCAAGAT
Statistics
Matches: 948, Mismatches: 88, Indels: 81
0.85 0.08 0.07
Matches are distributed among these distances:
395 140 0.15
396 111 0.12
397 66 0.07
398 5 0.01
400 2 0.00
401 1 0.00
402 3 0.00
404 1 0.00
409 3 0.00
411 2 0.00
412 2 0.00
414 7 0.01
415 5 0.01
416 6 0.01
417 169 0.18
418 64 0.07
420 3 0.00
421 1 0.00
423 1 0.00
424 61 0.06
425 143 0.15
426 36 0.04
427 3 0.00
428 110 0.12
429 3 0.00
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (413 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTCAAATGAATTTATGAAAAATGATGTTTTAAGAAG
ATGGAACTTTTGAAAACGAAGAATGCGATTTTCAAAATTTACATTTATAAGTCCTTCGGGCCATC
AGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGA
TAAGTCCTTCGGGCCATCCATAAACCTTCGGGTAGGATGTTTTCAAATGAAATTGAAAATGAAAA
AATGAAGAAGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTTCACAATTTATAAGTCCC
TCAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAG
AACAAGATGATAAATCCTTCAGG
Found at i:1355379 original size:181 final size:182
Alignment explanation
Indices: 1355069--1355440 Score: 584
Period size: 181 Copynumber: 2.0 Consensus size: 182
1355059 AAATGAAAAG
* * * *
1355069 TGATGTTTTAAGAATATGGAAGTTTTGAAAAAGAAGAATGTGATTTTCAAAATTTCACAGTTTAT
1 TGATGTTTTAAGAAGATGAAAGTTTTGAAAAAGAAGAATGCGATTTTCAAAATTTCACAATTTAT
* * * *
1355134 AAGTCCTTCGGGCCATCAGTAATTCTTTCGAGCATGATGCTTAAATCCTTCGTGTCATCTGTAAG
66 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTAATCTGTAAG
*
1355199 CCTTTAGAGCAAGATGATAAGTCCTTCGGGCAATTCATAAAACCTTCGGGTA
131 CCTTTAGAGCAAGATGATAAGTCCTTCGGGCAATCCATAAAACCTTCGGGTA
* *
1355251 TGATG-TTTAAGAAGATGAAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTAT
1 TGATGTTTTAAGAAGATGAAAGTTTTGAAAAAGAAGAATGCGATTTTCAAAATTTCACAATTTAT
*
1355315 AAGTCCTTCGGGCCATTAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTAATCTGTAAG
66 AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTAATCTGTAAG
* * *
1355380 CCTTTAGAGTAAGATGATAAGTCTTTCGGGCCATCCATAAAACCTTCGGGTA
131 CCTTTAGAGCAAGATGATAAGTCCTTCGGGCAATCCATAAAACCTTCGGGTA
* *
1355432 GGATATTTT
1 TGATGTTTT
1355441 CACATGAATT
Statistics
Matches: 172, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 164 0.95
182 8 0.05
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (182 bp):
TGATGTTTTAAGAAGATGAAAGTTTTGAAAAAGAAGAATGCGATTTTCAAAATTTCACAATTTAT
AAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCATTCGGGTAATCTGTAAG
CCTTTAGAGCAAGATGATAAGTCCTTCGGGCAATCCATAAAACCTTCGGGTA
Found at i:1355598 original size:43 final size:41
Alignment explanation
Indices: 1355528--1355630 Score: 100
Period size: 43 Copynumber: 2.5 Consensus size: 41
1355518 TTCACAATTT
* * **
1355528 ATAAGTCCTTCGGGCCATCAGTAAGTCT-TTCGAGCACTATG
1 ATAAATCCTTCGGGTCATCAGTAAGTCTCTT-GAGCAAGATG
* ** *
1355569 CTTAAAATCCTTCGGGTCATTTGTGAGTCTCTTGAGCAAGATG
1 -AT-AAATCCTTCGGGTCATCAGTAAGTCTCTTGAGCAAGATG
1355612 ATAAATCCTTCGGGTCATC
1 ATAAATCCTTCGGGTCATC
1355631 CATAAGACCT
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
41 16 0.33
42 2 0.04
43 29 0.59
44 2 0.04
ACGTcount: A:0.24, C:0.22, G:0.21, T:0.32
Consensus pattern (41 bp):
ATAAATCCTTCGGGTCATCAGTAAGTCTCTTGAGCAAGATG
Found at i:1355669 original size:56 final size:56
Alignment explanation
Indices: 1355605--1355712 Score: 171
Period size: 56 Copynumber: 1.9 Consensus size: 56
1355595 GTCTCTTGAG
* *
1355605 CAAGATGATAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAGGATGTTTTGCAC
1 CAAGATGATAAATCCTTCGGGCCATCCATAAGACCTTCGAGCAGGATGTTTTGCAC
* * *
1355661 CAAGATGATAAGTCCTTCGGGCCATCCATGAGACCTTCGAGTAGGATGTTTT
1 CAAGATGATAAATCCTTCGGGCCATCCATAAGACCTTCGAGCAGGATGTTTT
1355713 CACATGAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.26, C:0.22, G:0.24, T:0.28
Consensus pattern (56 bp):
CAAGATGATAAATCCTTCGGGCCATCCATAAGACCTTCGAGCAGGATGTTTTGCAC
Found at i:1366693 original size:18 final size:18
Alignment explanation
Indices: 1366630--1366907 Score: 98
Period size: 18 Copynumber: 15.5 Consensus size: 18
1366620 TATATGTACA
*
1366630 ATAAA-ATAATATATAAT
1 ATAAATATACTATATAAT
* * *
1366647 AAATAATACATCTAAATATAT
1 ATA-AATATA-CTATATA-AT
*
1366668 ATATATATACTATATAAT
1 ATAAATATACTATATAAT
* *
1366686 ATAAATATAATATGCGTGAAT
1 ATAAATATACTAT--AT-AAT
* *
1366707 AT--ATA-ACGACATAAT
1 ATAAATATACTATATAAT
* * *
1366722 ATATACACACTATATAAT
1 ATAAATATACTATATAAT
* *
1366740 ATAAGTATATTATAGT-AT
1 ATAAATATACTATA-TAAT
1366758 ATAAATATA-TAATATAAT
1 ATAAATATACT-ATATAAT
***
1366776 ACGTATATACTATATAAT
1 ATAAATATACTATATAAT
*
1366794 ATAAATAGAC---A-AA-
1 ATAAATATACTATATAAT
1366807 ATAAATA-AC-ATAATACAT
1 ATAAATATACTAT-ATA-AT
* *
1366825 ATATATATACTATAGAAT
1 ATAAATATACTATATAAT
* *
1366843 AT-ATTATACAATATAAT
1 ATAAATATACTATATAAT
*
1366860 ATAAATATATAGTCATATAAT
1 AT-AA-ATATACT-ATATAAT
****
1366881 ACGTTTATACTATATAAT
1 ATAAATATACTATATAAT
1366899 ATAAATATA
1 ATAAATATA
1366908 ATAATATACA
Statistics
Matches: 186, Mismatches: 49, Indels: 51
0.65 0.17 0.18
Matches are distributed among these distances:
12 2 0.01
13 7 0.04
14 2 0.01
15 7 0.04
16 2 0.01
17 20 0.11
18 90 0.48
19 23 0.12
20 16 0.09
21 17 0.09
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (18 bp):
ATAAATATACTATATAAT
Found at i:1366766 original size:8 final size:7
Alignment explanation
Indices: 1366750--1366922 Score: 66
Period size: 7 Copynumber: 23.3 Consensus size: 7
1366740 ATAAGTATAT
*
1366750 TATAGTA
1 TATAATA
1366757 TATAAATA
1 TAT-AATA
1366765 TATAATA
1 TATAATA
*
1366772 TAATACGTA
1 T-ATA-ATA
*
1366781 TATACTA
1 TATAATA
1366788 TATAATA
1 TATAATA
1366795 TA-AATA
1 TATAATA
* * *
1366801 GACAAAA
1 TATAATA
1366808 TA-AATAA
1 TATAAT-A
*
1366815 CATAATA
1 TATAATA
*
1366822 CATATATA
1 TATA-ATA
*
1366830 TATACTA
1 TATAATA
*
1366837 TAGAATA
1 TATAATA
*
1366844 TATTATACAA
1 TA-TA-A-TA
1366854 TATAATA
1 TATAATA
1366861 TA-AATA
1 TATAATA
*
1366867 TATAGTCA
1 TATAAT-A
1366875 TATAATA
1 TATAATA
*
1366882 CGTTTATACTA
1 ----TATAATA
1366893 TATAATA
1 TATAATA
1366900 TA-AATA
1 TATAATA
1366906 TAATAATA
1 T-ATAATA
*
1366914 TACAATA
1 TATAATA
1366921 TA
1 TA
1366923 AACAAGGTTG
Statistics
Matches: 127, Mismatches: 21, Indels: 36
0.69 0.11 0.20
Matches are distributed among these distances:
6 18 0.14
7 60 0.47
8 34 0.27
9 6 0.05
10 3 0.02
11 6 0.05
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.36
Consensus pattern (7 bp):
TATAATA
Found at i:1366772 original size:23 final size:23
Alignment explanation
Indices: 1366732--1366881 Score: 73
Period size: 23 Copynumber: 6.4 Consensus size: 23
1366722 ATATACACAC
*
1366732 TATATAATATA-AGTATATTATA-G
1 TATATAATATATA--ATATAATACG
1366755 TATATAAATATATAATATAATACG
1 TATAT-AATATATAATATAATACG
*
1366779 TATATACTATATAATATAAATA-G
1 TATATAATATATAATAT-AATACG
* * * * *
1366802 -ACAAAATAAATAACATAATACA
1 TATATAATATATAATATAATACG
1366824 TATATATATACTATAGAATATATTATAC-
1 TATATA-ATA-TAT--AATATA--ATACG
*
1366852 AATATAATATA-AATAT-ATA-G
1 TATATAATATATAATATAATACG
1366872 TCATATAATA
1 T-ATATAATA
1366882 CGTTTATACT
Statistics
Matches: 99, Mismatches: 14, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
20 3 0.03
21 12 0.12
22 11 0.11
23 32 0.32
24 19 0.19
25 3 0.03
26 2 0.02
27 8 0.08
28 5 0.05
29 4 0.04
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.37
Consensus pattern (23 bp):
TATATAATATATAATATAATACG
Found at i:1366791 original size:49 final size:48
Alignment explanation
Indices: 1366738--1366901 Score: 118
Period size: 49 Copynumber: 3.2 Consensus size: 48
1366728 ACACTATATA
1366738 ATATAAGTATATTATAGTATATAAATATATAATATAATACGTATATACT
1 ATATAA-TATATTATAGTATATAAATATATAATATAATACGTATATACT
* * * **
1366787 ATATAATATA-AATAG-ACA-AAATAAATAACATAATACATATATATATACT
1 ATATAATATATTATAGTATATAAATATAT-A-AT-ATA-ATACGTATATACT
* * *
1366836 ATAGAATATATTATACAATATAATATAAATATATAGTCATATAATACGTTTATACT
1 ATATAATATATTAT---A-GT-ATATAAATATATA---ATATAATACGTATATACT
1366892 ATATAATATA
1 ATATAATATA
1366902 AATATAATAA
Statistics
Matches: 87, Mismatches: 14, Indels: 21
0.71 0.11 0.17
Matches are distributed among these distances:
45 7 0.08
46 3 0.03
47 6 0.07
48 7 0.08
49 26 0.30
50 2 0.02
53 1 0.01
56 22 0.25
57 10 0.11
58 3 0.03
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.37
Consensus pattern (48 bp):
ATATAATATATTATAGTATATAAATATATAATATAATACGTATATACT
Found at i:1366868 original size:39 final size:39
Alignment explanation
Indices: 1366816--1366922 Score: 105
Period size: 39 Copynumber: 2.8 Consensus size: 39
1366806 AATAAATAAC
* * *
1366816 ATAATACATATATATATACTATAGAATATATTATACAAT
1 ATAATATAAATATATATACTATACAATATATTATACAAT
* *
1366855 ATAATATAAATATATAGT-C-ATATAATACGT-TTATACTAT
1 ATAATATAAATATATA-TACTATACAATA--TATTATACAAT
*
1366894 ATAATATAAATATA-ATAATATACAATATA
1 ATAATATAAATATATATACTATACAATATA
1366923 AACAAGGTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
37 2 0.04
38 8 0.14
39 44 0.79
40 2 0.04
ACGTcount: A:0.52, C:0.07, G:0.03, T:0.38
Consensus pattern (39 bp):
ATAATATAAATATATATACTATACAATATATTATACAAT
Found at i:1369267 original size:54 final size:54
Alignment explanation
Indices: 1369185--1369292 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
1369175 AGCTTTATGT
*
1369185 TAAAATTGTTCACAAGTGGAATCCATTGTAACACCCCAACCCGTACGCTACCCG
1 TAAAATTGTTCACAAGTAGAATCCATTGTAACACCCCAACCCGTACGCTACCCG
1369239 TAAAATTGTTCACAAGTAGAATCCATTGTAACACCCCAACCCGTACGCTACCCG
1 TAAAATTGTTCACAAGTAGAATCCATTGTAACACCCCAACCCGTACGCTACCCG
1369293 GATACAAGTC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.31, G:0.14, T:0.22
Consensus pattern (54 bp):
TAAAATTGTTCACAAGTAGAATCCATTGTAACACCCCAACCCGTACGCTACCCG
Found at i:1370242 original size:24 final size:24
Alignment explanation
Indices: 1370197--1370266 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
1370187 CTCGTATAAA
* * *
1370197 ATGCACCGAAGTGTCGCGTAGAAT
1 ATGCACCGAAGTGCCACATAGAAT
1370221 ATGCACCGAAGTGCCACATAGAAT
1 ATGCACCGAAGTGCCACATAGAAT
*
1370245 GT-C-CCGAAG-GACCACATAGAAT
1 ATGCACCGAAGTG-CCACATAGAAT
1370267 TATCCCATAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 1 0.02
22 17 0.41
23 1 0.02
24 22 0.54
ACGTcount: A:0.34, C:0.24, G:0.24, T:0.17
Consensus pattern (24 bp):
ATGCACCGAAGTGCCACATAGAAT
Found at i:1370278 original size:23 final size:22
Alignment explanation
Indices: 1370215--1370285 Score: 74
Period size: 22 Copynumber: 3.1 Consensus size: 22
1370205 AAGTGTCGCG
1370215 TAGAATATGCACCGAAGTG-CCACA
1 TAGAATAT-C-CCGAAG-GACCACA
*
1370239 TAGAATGTCCCGAAGGACCACA
1 TAGAATATCCCGAAGGACCACA
1370261 TAGAATTATCCC-ATAGGACCACA
1 TAGAA-TATCCCGA-AGGACCACA
1370284 TA
1 TA
1370286 TATGTTCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 1 0.02
22 17 0.40
23 17 0.40
24 7 0.17
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (22 bp):
TAGAATATCCCGAAGGACCACA
Found at i:1370328 original size:19 final size:21
Alignment explanation
Indices: 1370316--1370356 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1370306 ATATATCCTG
1370316 AAGGATCACATATATGCTCCC
1 AAGGATCACATATATGCTCCC
1370337 AAGGATCACATATATG-TCCC
1 AAGGATCACATATATGCTCCC
1370357 GAAGAACCGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (21 bp):
AAGGATCACATATATGCTCCC
Found at i:1373368 original size:14 final size:14
Alignment explanation
Indices: 1373343--1373377 Score: 61
Period size: 14 Copynumber: 2.4 Consensus size: 14
1373333 CCCATCAGAC
1373343 TTAATCTCAAAATCT
1 TTAAT-TCAAAATCT
1373358 TTAATTCAAAATCT
1 TTAATTCAAAATCT
1373372 TTAATT
1 TTAATT
1373378 TCTTCATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAATTCAAAATCT
Found at i:1375553 original size:20 final size:20
Alignment explanation
Indices: 1375528--1375568 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1375518 AATAACTTAC
1375528 TAAATTCTTTCCTCTACTCT
1 TAAATTCTTTCCTCTACTCT
1375548 TAAATTCTTTCCTCTACTCT
1 TAAATTCTTTCCTCTACTCT
1375568 T
1 T
1375569 CTTTTTCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.29, G:0.00, T:0.51
Consensus pattern (20 bp):
TAAATTCTTTCCTCTACTCT
Found at i:1379752 original size:19 final size:19
Alignment explanation
Indices: 1379724--1379761 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
1379714 AATCTATTCA
*
1379724 GAGAATAATAAAATAAAAT
1 GAGAAAAATAAAATAAAAT
1379743 GAGAAAAATAAAATAAAAT
1 GAGAAAAATAAAATAAAAT
1379762 TAAGCATCTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (19 bp):
GAGAAAAATAAAATAAAAT
Found at i:1383797 original size:21 final size:21
Alignment explanation
Indices: 1383771--1383818 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1383761 GAATTTGGAA
* *
1383771 CTTTTCCTGGGATGTAACTAG
1 CTTTTCCTGGGACGTAACCAG
*
1383792 CTTTTCCTGGGACGTAACCAT
1 CTTTTCCTGGGACGTAACCAG
1383813 CTTTTC
1 CTTTTC
1383819 TTACGAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.40
Consensus pattern (21 bp):
CTTTTCCTGGGACGTAACCAG
Found at i:1385380 original size:23 final size:21
Alignment explanation
Indices: 1385353--1385394 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1385343 TTTAAATTGT
1385353 TTAAAGAAATCAAAAGATAAATA
1 TTAAAGAAAT-AAAA-ATAAATA
*
1385376 TTAAATAAATAAAAATAAA
1 TTAAAGAAATAAAAATAAA
1385395 ATAGATTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 4 0.22
23 9 0.50
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (21 bp):
TTAAAGAAATAAAAATAAATA
Found at i:1388958 original size:26 final size:26
Alignment explanation
Indices: 1388925--1388974 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
1388915 GCATGGTCTT
*
1388925 GTGCATCGATGCATCAAATGCATTGA
1 GTGCATCGATGCATAAAATGCATTGA
1388951 GTGCATCGATGCATAAAATGCATT
1 GTGCATCGATGCATAAAATGCATT
1388975 CGATGTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (26 bp):
GTGCATCGATGCATAAAATGCATTGA
Found at i:1400160 original size:17 final size:18
Alignment explanation
Indices: 1400138--1400213 Score: 63
Period size: 18 Copynumber: 4.3 Consensus size: 18
1400128 ATAAATATTT
1400138 ATATATACAATA-AAATA
1 ATATATACAATATAAATA
*
1400155 ATATATAATAATATATAATA
1 ATATAT-ACAATATA-AATA
1400175 A-ATAATAC-ATATAAATA
1 ATAT-ATACAATATAAATA
*
1400192 TGTATATA-AATAT-AATA
1 -ATATATACAATATAAATA
1400209 ATATA
1 ATATA
1400214 ATAATATACT
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
16 4 0.08
17 14 0.29
18 17 0.35
19 6 0.12
20 7 0.15
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.36
Consensus pattern (18 bp):
ATATATACAATATAAATA
Found at i:1400166 original size:10 final size:10
Alignment explanation
Indices: 1400151--1400219 Score: 62
Period size: 10 Copynumber: 7.4 Consensus size: 10
1400141 TATACAATAA
1400151 AATAATATAT
1 AATAATATAT
1400161 AATAATATAT
1 AATAATATAT
1400171 AAT-A-A-AT
1 AATAATATAT
1400178 AATACATATA-
1 AATA-ATATAT
*
1400188 AAT-ATGTAT
1 AATAATATAT
1400197 -ATAA-ATAT
1 AATAATATAT
1400205 AATAATATAAT
1 AATAATAT-AT
1400216 AATA
1 AATA
1400220 TACTATTTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 17
0.72 0.03 0.25
Matches are distributed among these distances:
7 5 0.10
8 10 0.21
9 7 0.15
10 19 0.40
11 7 0.15
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (10 bp):
AATAATATAT
Found at i:1400180 original size:14 final size:13
Alignment explanation
Indices: 1400137--1400221 Score: 68
Period size: 14 Copynumber: 6.3 Consensus size: 13
1400127 GATAAATATT
1400137 TATATATACAATAA
1 TATATATA-AATAA
*
1400151 AATAATATATAATAA
1 TAT-ATATA-AATAA
1400166 TATATAATAAATAA
1 TATAT-ATAAATAA
*
1400180 TACATATAAAT-A
1 TATATATAAATAA
*
1400192 TGTATATAAAT-A
1 TATATATAAATAA
1400204 TA-ATAATATAATAA
1 TATAT-ATA-AATAA
1400218 TATA
1 TATA
1400222 CTATTTAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 11
0.76 0.09 0.14
Matches are distributed among these distances:
11 2 0.03
12 15 0.26
13 9 0.16
14 16 0.28
15 16 0.28
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.36
Consensus pattern (13 bp):
TATATATAAATAA
Found at i:1400211 original size:8 final size:8
Alignment explanation
Indices: 1400146--1400221 Score: 59
Period size: 8 Copynumber: 9.1 Consensus size: 8
1400136 TTATATATAC
*
1400146 AATAAAAT
1 AATAATAT
1400154 AAT-ATAT
1 AATAATAT
1400161 AATAATAT
1 AATAATAT
1400169 -ATAATAAAT
1 AATAAT--AT
1400178 AATACATAT
1 AATA-ATAT
*
1400187 AA-ATATGT
1 AATA-ATAT
1400195 ATATAAATAT
1 A-AT-AATAT
1400205 AATAATAT
1 AATAATAT
1400213 AATAATAT
1 AATAATAT
1400221 A
1 A
1400222 CTATTTAAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
7 11 0.20
8 26 0.46
9 9 0.16
10 7 0.12
11 3 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (8 bp):
AATAATAT
Found at i:1400555 original size:24 final size:25
Alignment explanation
Indices: 1400509--1400555 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
1400499 TATATTTTTA
* *
1400509 ATTTATTTAAAATTTAATGTATACG
1 ATTTATTTAAAATATAATATATACG
*
1400534 ATTTATTT-GAATATAATATATA
1 ATTTATTTAAAATATAATATATA
1400556 ATTTGATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 11 0.58
25 8 0.42
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.49
Consensus pattern (25 bp):
ATTTATTTAAAATATAATATATACG
Found at i:1400674 original size:2 final size:2
Alignment explanation
Indices: 1400669--1400747 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
1400659 TATGTGTGTG
1400669 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1400711 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1400748 TATGATATCA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1401709 original size:39 final size:39
Alignment explanation
Indices: 1401660--1401741 Score: 121
Period size: 39 Copynumber: 2.1 Consensus size: 39
1401650 TATAATTTTC
*
1401660 AAATTATTTCA-CTTTAACATTCTAAATTCTAAATTTCTT
1 AAATTATTTCATC-ATAACATTCTAAATTCTAAATTTCTT
* *
1401699 AAATTTTTTCATCATAACATTCTAAATTCTCAATTTCTT
1 AAATTATTTCATCATAACATTCTAAATTCTAAATTTCTT
1401738 AAAT
1 AAAT
1401742 CTTAAATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
39 38 0.97
40 1 0.03
ACGTcount: A:0.37, C:0.16, G:0.00, T:0.48
Consensus pattern (39 bp):
AAATTATTTCATCATAACATTCTAAATTCTAAATTTCTT
Found at i:1402043 original size:13 final size:13
Alignment explanation
Indices: 1402025--1402050 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1402015 AATAATTATT
1402025 TAATTTTTTTGTA
1 TAATTTTTTTGTA
1402038 TAATTTTTTTGTA
1 TAATTTTTTTGTA
1402051 ATGTTTAATT
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:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (13 bp):
TAATTTTTTTGTA
Found at i:1407830 original size:67 final size:67
Alignment explanation
Indices: 1407722--1407855 Score: 268
Period size: 67 Copynumber: 2.0 Consensus size: 67
1407712 CATTCTTTAT
1407722 CTGATACGGATAATGGATGATGCAAATTAGATAGGAAAAGCACCCCCGGTACTTGTTAATTCCTT
1 CTGATACGGATAATGGATGATGCAAATTAGATAGGAAAAGCACCCCCGGTACTTGTTAATTCCTT
1407787 GG
66 GG
1407789 CTGATACGGATAATGGATGATGCAAATTAGATAGGAAAAGCACCCCCGGTACTTGTTAATTCCTT
1 CTGATACGGATAATGGATGATGCAAATTAGATAGGAAAAGCACCCCCGGTACTTGTTAATTCCTT
1407854 GG
66 GG
1407856 AAATATGTTG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (67 bp):
CTGATACGGATAATGGATGATGCAAATTAGATAGGAAAAGCACCCCCGGTACTTGTTAATTCCTT
GG
Found at i:1416240 original size:31 final size:32
Alignment explanation
Indices: 1416187--1416268 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
1416177 GAGCACTTTC
* * *
1416187 CTTTGCTTGCTTTCTTTT-TGAA-TTTCTTTTT
1 CTTTTCTT-CTTTTTTTTCTGAATTTTCTTCTT
1416218 CTTTTCTTCTTTTTTTTCTGAATTTTCTTCTT
1 CTTTTCTTCTTTTTTTTCTGAATTTTCTTCTT
*
1416250 CTTTT-TGTCTTTTCTTTCT
1 CTTTTCT-TCTTTTTTTTCT
1416269 TTTTGTACTC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
30 8 0.18
31 12 0.27
32 24 0.55
ACGTcount: A:0.05, C:0.18, G:0.06, T:0.71
Consensus pattern (32 bp):
CTTTTCTTCTTTTTTTTCTGAATTTTCTTCTT
Done.