Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007822.1 Hibiscus syriacus cultivar Beakdansim tig00110159_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: 1828853
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 10
Found at i:1051841 original size:50 final size:50
Alignment explanation
Indices: 1051738--1051850 Score: 138
Period size: 50 Copynumber: 2.3 Consensus size: 50
1051728 TAGCGTAGAT
* * * * *
1051738 CAGGGGGCGCGCTATATCCACGTGGCGCCAGATAACTGTATATCGCGGGG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAATAACTATATAGCGCAGGG
* * *
1051788 CAGGGGGTGCGCTATACCCACGTGGCGCCAAATCAGC-ATATAGCGCAGTG
1 CAGGGGGCGCGCTATACCCACGTGGCGCCAAAT-AACTATATAGCGCAGGG
1051838 CAGGGGGCGCGCT
1 CAGGGGGCGCGCT
1051851 TTTCTGCTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 51 0.96
51 2 0.04
ACGTcount: A:0.20, C:0.27, G:0.36, T:0.16
Consensus pattern (50 bp):
CAGGGGGCGCGCTATACCCACGTGGCGCCAAATAACTATATAGCGCAGGG
Found at i:1052368 original size:38 final size:36
Alignment explanation
Indices: 1052325--1052398 Score: 87
Period size: 39 Copynumber: 2.0 Consensus size: 36
1052315 TTTCAAAAAT
*
1052325 CGGGTCAAGTTCGGA-TCGGGTGGAGGATATATATTATG
1 CGGGTCAAG-TCAGATTCGGGTGGAGGA-AT-TATTATG
*
1052363 CGGGTCGAGTCAGATTTCGGGTGGAGGAATTATTAT
1 CGGGTCAAGTCAGA-TTCGGGTGGAGGAATTATTAT
1052399 TCTCGAATAG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 10 0.31
38 10 0.31
39 12 0.38
ACGTcount: A:0.23, C:0.11, G:0.36, T:0.30
Consensus pattern (36 bp):
CGGGTCAAGTCAGATTCGGGTGGAGGAATTATTATG
Found at i:1053000 original size:2 final size:2
Alignment explanation
Indices: 1052993--1053025 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1052983 ATGTGGTTCG
1052993 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1053026 TATATAGTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1069894 original size:34 final size:34
Alignment explanation
Indices: 1069856--1069921 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1069846 CACATATTTG
*
1069856 AAGAAAAATTACAATAAATTTATATATTCTTAGT
1 AAGAAAAATTACAATAAATTTAAATATTCTTAGT
* **
1069890 AAGAAAAATTACATTATTTTTAAATATTCTTA
1 AAGAAAAATTACAATAAATTTAAATATTCTTA
1069922 ATATATGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (34 bp):
AAGAAAAATTACAATAAATTTAAATATTCTTAGT
Found at i:1075519 original size:13 final size:13
Alignment explanation
Indices: 1075490--1075524 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1075480 ATAACTAATA
*
1075490 ATATTAAAT-ATT
1 ATATTAAATAAAT
1075502 ATATTAAATAAAT
1 ATATTAAATAAAT
1075515 ATATTAAATA
1 ATATTAAATA
1075525 TATTTATGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTAAATAAAT
Found at i:1076215 original size:15 final size:15
Alignment explanation
Indices: 1076146--1076217 Score: 56
Period size: 18 Copynumber: 4.5 Consensus size: 15
1076136 TATTATTTTA
1076146 ATAAAAAATAAT-AT
1 ATAAAAAATAATAAT
* *
1076160 TTACATAAATATATTAAT
1 ATA-A-AAA-ATAATAAT
1076178 ATAAAAAATAATAACT
1 ATAAAAAATAATAA-T
*
1076194 ATTTAAAAAATACTAAT
1 A--TAAAAAATAATAAT
1076211 ATAAAAA
1 ATAAAAA
1076218 TAAATTTCTT
Statistics
Matches: 46, Mismatches: 5, Indels: 13
0.72 0.08 0.20
Matches are distributed among these distances:
14 2 0.04
15 13 0.28
16 8 0.17
17 7 0.15
18 16 0.35
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAAAATAATAAT
Found at i:1076220 original size:32 final size:35
Alignment explanation
Indices: 1076148--1076217 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 35
1076138 TTATTTTAAT
*
1076148 AAAA-AATAATATTTACATAAATATATTAATATAA
1 AAAATAATAATATTTACATAAATATACTAATATAA
1076182 AAAATAATAACTATTTA-A-AAA-ATACTAATATAA
1 AAAATAATAA-TATTTACATAAATATACTAATATAA
1076215 AAA
1 AAA
1076218 TAAATTTCTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
33 14 0.42
34 7 0.21
35 6 0.18
36 6 0.18
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.31
Consensus pattern (35 bp):
AAAATAATAATATTTACATAAATATACTAATATAA
Found at i:1085941 original size:14 final size:14
Alignment explanation
Indices: 1085922--1085950 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1085912 GGAAGGCCCT
1085922 TGGAAAATATTGGA
1 TGGAAAATATTGGA
1085936 TGGAAAATATTGGA
1 TGGAAAATATTGGA
1085950 T
1 T
1085951 CACTATATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.28, T:0.31
Consensus pattern (14 bp):
TGGAAAATATTGGA
Found at i:1092911 original size:50 final size:48
Alignment explanation
Indices: 1092856--1092952 Score: 167
Period size: 50 Copynumber: 2.0 Consensus size: 48
1092846 GTACGTGTAG
*
1092856 ATGAAAGAAAGTTTGCCACAGACAAAGTATCCACAACCTAAAACCAAAAA
1 ATGAAAGAAAGTTTGCCACAGAC-AAGCATCCACAACCT-AAACCAAAAA
1092906 ATGAAAGAAAGTTTGCCACAGACAAGCATCCACAACCTAAACCAAAA
1 ATGAAAGAAAGTTTGCCACAGACAAGCATCCACAACCTAAACCAAAA
1092953 CTCTTCCACA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 9 0.20
49 14 0.30
50 23 0.50
ACGTcount: A:0.51, C:0.24, G:0.12, T:0.13
Consensus pattern (48 bp):
ATGAAAGAAAGTTTGCCACAGACAAGCATCCACAACCTAAACCAAAAA
Found at i:1100856 original size:41 final size:44
Alignment explanation
Indices: 1100811--1100892 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
1100801 TATGATAATT
1100811 AATAAGATAA-T-ATCTA-AATGTATTAATAAATAATAAAAAAC
1 AATAAGATAACTAATCTATAATGTATTAATAAATAATAAAAAAC
* * * *
1100852 AATAAGTTAACTAATCTATTATTTTTTAATAAATAATAAAA
1 AATAAGATAACTAATCTATAATGTATTAATAAATAATAAAA
1100893 TATTATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 9 0.26
42 1 0.03
43 5 0.15
44 19 0.56
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (44 bp):
AATAAGATAACTAATCTATAATGTATTAATAAATAATAAAAAAC
Found at i:1103640 original size:21 final size:19
Alignment explanation
Indices: 1103611--1103665 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
1103601 GAAAAGGTTG
*
1103611 AAAAGTTGAAAAAGTTAGAA
1 AAAAATTGAAAAAGTTA-AA
1103631 TAAAAATTGAAAAAGTTAAA
1 -AAAAATTGAAAAAGTTAAA
1103651 AAGAAAGTTGAAAAA
1 AA-AAA-TTGAAAAA
1103666 AACGTGTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 24 0.77
ACGTcount: A:0.64, C:0.00, G:0.16, T:0.20
Consensus pattern (19 bp):
AAAAATTGAAAAAGTTAAA
Found at i:1103905 original size:43 final size:44
Alignment explanation
Indices: 1103836--1103931 Score: 108
Period size: 43 Copynumber: 2.2 Consensus size: 44
1103826 ATATAAAATG
*
1103836 ATAAATATAATACTTAAATAAAAGATA-ACCGAATAAAATAATTA
1 ATAAATATAATACTTAAATAAAAGATATA-CAAATAAAATAATTA
* * *
1103880 ATAAATATACATA-TT-AATAATAGATATATAAATAAAATATTTA
1 ATAAATATA-ATACTTAAATAAAAGATATACAAATAAAATAATTA
*
1103923 AAAAATATA
1 ATAAATATA
1103932 TATGTATATA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
43 30 0.67
44 12 0.27
45 3 0.07
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (44 bp):
ATAAATATAATACTTAAATAAAAGATATACAAATAAAATAATTA
Found at i:1103919 original size:13 final size:13
Alignment explanation
Indices: 1103867--1103932 Score: 57
Period size: 12 Copynumber: 4.9 Consensus size: 13
1103857 AAGATAACCG
1103867 AATAAAATA-ATT
1 AATAAAATATATT
1103879 AATAAATATACATATT
1 AATAAA-AT--ATATT
*
1103895 AATAATAGATATATA
1 AATAA-A-ATATATT
1103910 AATAAAATAT-TT
1 AATAAAATATATT
1103922 AA-AAAATATAT
1 AATAAAATATAT
1103933 ATGTATATAT
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
11 7 0.16
12 10 0.22
13 6 0.13
14 1 0.02
15 10 0.22
16 8 0.18
17 3 0.07
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
AATAAAATATATT
Found at i:1104699 original size:13 final size:13
Alignment explanation
Indices: 1104683--1104707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1104673 GTAAAAACAG
1104683 TAAATAAAATAAA
1 TAAATAAAATAAA
1104696 TAAATAAAATAA
1 TAAATAAAATAA
1104708 GAAGAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:1114926 original size:13 final size:13
Alignment explanation
Indices: 1114910--1114934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1114900 GTAAAAATAG
1114910 TAAATAAAATAAA
1 TAAATAAAATAAA
1114923 TAAATAAAATAA
1 TAAATAAAATAA
1114935 GAAGAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAAAATAAA
Found at i:1120032 original size:42 final size:42
Alignment explanation
Indices: 1119973--1120056 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
1119963 TTGATATACA
*
1119973 GCAAAATGTCGTAGTACCAAGGCTTAGTGTCTTTTACTTCTT
1 GCAAAATATCGTAGTACCAAGGCTTAGTGTCTTTTACTTCTT
1120015 GCAAAATATCGTAGTACCAAGGCTTAGTGTCTTTTACTTCTT
1 GCAAAATATCGTAGTACCAAGGCTTAGTGTCTTTTACTTCTT
1120057 CAATCTGGTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.19, G:0.18, T:0.38
Consensus pattern (42 bp):
GCAAAATATCGTAGTACCAAGGCTTAGTGTCTTTTACTTCTT
Found at i:1124893 original size:14 final size:14
Alignment explanation
Indices: 1124874--1124908 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1124864 AATTGCCACC
1124874 AGGTGCCCAAAGTA
1 AGGTGCCCAAAGTA
**
1124888 AGGTGCCTGAAGTA
1 AGGTGCCCAAAGTA
1124902 AGGTGCC
1 AGGTGCC
1124909 TTCAGAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.29, C:0.20, G:0.34, T:0.17
Consensus pattern (14 bp):
AGGTGCCCAAAGTA
Found at i:1124909 original size:14 final size:14
Alignment explanation
Indices: 1124883--1124909 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1124873 CAGGTGCCCA
1124883 AAGTAAGGTGCCTG
1 AAGTAAGGTGCCTG
1124897 AAGTAAGGTGCCT
1 AAGTAAGGTGCCT
1124910 TCAGAGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.15, G:0.33, T:0.22
Consensus pattern (14 bp):
AAGTAAGGTGCCTG
Found at i:1131054 original size:16 final size:16
Alignment explanation
Indices: 1131029--1131093 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
1131019 TAATAAATAA
1131029 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
1131045 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
*
1131061 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
*
1131077 ACAAACATAAACGAAC
1 ACGAACATAAACGAAC
1131093 A
1 A
1131094 TAAACGTTGG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1131586 original size:14 final size:14
Alignment explanation
Indices: 1131569--1131600 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
1131559 AATAAACATA
1131569 AACGAACATAACCG
1 AACGAACATAACCG
1131583 AACGAACATAACCG
1 AACGAACATAACCG
1131597 AACG
1 AACG
1131601 TTCACGAACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.28, G:0.16, T:0.06
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:1135901 original size:30 final size:31
Alignment explanation
Indices: 1135867--1135932 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
1135857 TTAAAATTTA
* *
1135867 CAATAC-ATTCCCTAACATTAAGTCTGTTTG
1 CAATACAATCCCCCAACATTAAGTCTGTTTG
*
1135897 CAATACAATCCCCCAACATTTAGTCTGTTTG
1 CAATACAATCCCCCAACATTAAGTCTGTTTG
1135928 CAATA
1 CAATA
1135933 TGGTTCCCGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 6 0.19
31 26 0.81
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.33
Consensus pattern (31 bp):
CAATACAATCCCCCAACATTAAGTCTGTTTG
Found at i:1136288 original size:2 final size:2
Alignment explanation
Indices: 1136281--1136322 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
1136271 CGAAATAAAC
*
1136281 AT AT AT AT TT AT AT AT -T AT AT AT AT CAT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT
1136323 TGTATAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1136303 original size:17 final size:17
Alignment explanation
Indices: 1136281--1136333 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
1136271 CGAAATAAAC
1136281 ATATATATTTATATATT
1 ATATATATTTATATATT
*
1136298 ATATATA-TCATATATAT
1 ATATATATTTATATAT-T
1136315 ATATATATTGTATA-ATT
1 ATATATATT-TATATATT
1136332 AT
1 AT
1136334 TATTATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 7 0.23
17 18 0.58
18 3 0.10
19 3 0.10
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
ATATATATTTATATATT
Found at i:1137589 original size:21 final size:22
Alignment explanation
Indices: 1137548--1137602 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 22
1137538 TTTAAAATCC
* *
1137548 TTTTATTAG-TTTTCTTATTAT
1 TTTTATTTGCTTTTATTATTAT
1137569 TTTTATTTGCTTTTATT-TTAT
1 TTTTATTTGCTTTTATTATTAT
*
1137590 ATTTATTTGCTTT
1 TTTTATTTGCTTT
1137603 GTTCATACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.16, C:0.05, G:0.05, T:0.73
Consensus pattern (22 bp):
TTTTATTTGCTTTTATTATTAT
Found at i:1138017 original size:14 final size:13
Alignment explanation
Indices: 1137991--1138026 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
1137981 GGTTTTTCTA
1137991 ATTTATTTTATTT
1 ATTTATTTTATTT
1138004 ATTTATTGTTATTT
1 ATTTATT-TTATTT
*
1138018 GTTTATTTT
1 ATTTATTTT
1138027 TAGAGAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (13 bp):
ATTTATTTTATTT
Found at i:1138245 original size:21 final size:21
Alignment explanation
Indices: 1138194--1138246 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1138184 AATCTGACTA
1138194 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* * * *
1138215 TTGCGTTGCGATTTTTCGAAT
1 TCGCATTGCGATTTTCCAAAT
*
1138236 TCGCAATGCGA
1 TCGCATTGCGA
1138247 ATATGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:1138261 original size:20 final size:20
Alignment explanation
Indices: 1138236--1138346 Score: 161
Period size: 20 Copynumber: 5.5 Consensus size: 20
1138226 TTTTTCGAAT
1138236 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
1138256 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
*
1138276 TTGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
* *
1138296 TCGCAATGTGAATATATAAA
1 TCGCAATGCGAATATGTAAA
* *
1138316 TCGCAATGCGATTATG-ACTA
1 TCGCAATGCGAATATGTA-AA
1138336 TCGCAATGCGA
1 TCGCAATGCGA
1138347 TTCTGACTAT
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
19 1 0.01
20 81 0.99
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.27
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:1138347 original size:20 final size:20
Alignment explanation
Indices: 1138315--1138422 Score: 135
Period size: 20 Copynumber: 5.4 Consensus size: 20
1138305 GAATATATAA
* *
1138315 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
*
1138335 ATCGCAATGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1138355 ATCGCAACGCGATTCTGATT
1 ATCGCAACGCGATTCTGACT
* * *
1138375 ATCGTAACGAGATTCTAACT
1 ATCGCAACGCGATTCTGACT
*
1138395 ATCGCAACGCAATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1138415 GTCGCAAC
1 ATCGCAAC
1138423 ACTGAATTTC
Statistics
Matches: 76, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 76 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1139296 original size:24 final size:24
Alignment explanation
Indices: 1139243--1139289 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1139233 GTATTCGAAA
*
1139243 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCAGAC
*
1139267 TTTGATCTTGGTCAATACTCAGA
1 TTTGATCTTGGTCAATACCCAGA
1139290 TATTGATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:1141681 original size:18 final size:18
Alignment explanation
Indices: 1141658--1141692 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1141648 AGAAAAAGGC
*
1141658 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
1141676 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
1141693 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:1141886 original size:20 final size:20
Alignment explanation
Indices: 1141861--1142031 Score: 165
Period size: 20 Copynumber: 8.8 Consensus size: 20
1141851 TTACACATTC
*
1141861 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1141881 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* ** * *
1141901 ATTTGATTATAACTACTC-A
1 ATTTGACTATCGCAACGCGA
*
1141920 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
1141935 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
1141955 ATTTGACTATAGCAACGAGA
1 ATTTGACTATCGCAACGCGA
*
1141975 ATTTGACTATCGCAACGTGA
1 ATTTGACTATCGCAACGCGA
* * *
1141995 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
1142015 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
1142032 AGAAAAGCGC
Statistics
Matches: 121, Mismatches: 24, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
14 6 0.05
15 3 0.02
19 3 0.02
20 109 0.90
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:1142019 original size:60 final size:60
Alignment explanation
Indices: 1141861--1142035 Score: 184
Period size: 60 Copynumber: 3.0 Consensus size: 60
1141851 TTACACATTC
* * * * * *
1141861 ATTTGAATATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGATTATAACTACTCA-A
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATAGCAAC-GAGA
*
1141921 A----A--ATCGCAACGCGAATTTGACTATCGCAATGCGAATTTGACTATAGCAACGAGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATAGCAACGAGA
* * * * *
1141975 ATTTGACTATCGCAACGTGAATTTGATTATCGCAACGGGTATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATAGCAACGAGA
1142035 A
1 A
1142036 AAGCGCAAAG
Statistics
Matches: 98, Mismatches: 10, Indels: 14
0.80 0.08 0.11
Matches are distributed among these distances:
53 1 0.01
54 47 0.48
56 1 0.01
58 1 0.01
60 48 0.49
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (60 bp):
ATTTGACTATCGCAACGCGAATTTGACTATCGCAACGCGAATTTGACTATAGCAACGAGA
Found at i:1142099 original size:20 final size:20
Alignment explanation
Indices: 1142074--1142112 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1142064 CACGAATTGA
1142074 CTTTCGCATTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
1142094 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
1142113 AGTTTAGCGT
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:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:1142125 original size:20 final size:20
Alignment explanation
Indices: 1142074--1142127 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1142064 CACGAATTGA
*
1142074 CTTTCGCATTGCGATTTTGG
1 CTTTAGCATTGCGATTTTGG
*
1142094 CTTTCGCATTGCGATTTTGAG
1 CTTTAGCATTGCGATTTTG-G
*
1142115 -TTTAGCGTTGCGA
1 CTTTAGCATTGCGA
1142128 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.13, C:0.19, G:0.26, T:0.43
Consensus pattern (20 bp):
CTTTAGCATTGCGATTTTGG
Found at i:1144291 original size:18 final size:18
Alignment explanation
Indices: 1144268--1144334 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 18
1144258 GAAACTTAAA
*
1144268 ATCGCAACACGAATGACT
1 ATCGCAACGCGAATGACT
1144286 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATGACT
*
1144306 ATCACAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
1144326 ATCGCAACG
1 ATCGCAACG
1144335 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
18 12 0.29
20 30 0.71
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:1144304 original size:20 final size:20
Alignment explanation
Indices: 1144279--1144334 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1144269 TCGCAACACG
1144279 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
*
1144299 AATGACTATCACAACGCGAA
1 AATGACTATCGCAACGCGAA
**
1144319 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
1144335 AGAGAATCGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:1144404 original size:20 final size:20
Alignment explanation
Indices: 1144379--1144424 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1144369 GATTCTTTCG
*
1144379 TTGCGATAGTTAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
1144399 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
1144419 TTGCGA
1 TTGCGA
1144425 AAGTAAACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:1146351 original size:20 final size:20
Alignment explanation
Indices: 1146328--1146415 Score: 79
Period size: 20 Copynumber: 4.5 Consensus size: 20
1146318 TCTGAAACTT
1146328 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
* *
1146348 AAAATTGCAACACGAAAAAG
1 AAAATCGCAACACGAAAATG
** **
1146368 ACTATCGCAACACGAATTTG
1 AAAATCGCAACACGAAAATG
** * *
1146388 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
1146407 AAAATCGCA
1 AAAATCGCA
1146416 TTACGATTCT
Statistics
Matches: 55, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
19 7 0.13
20 48 0.87
ACGTcount: A:0.48, C:0.23, G:0.15, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1146829 original size:22 final size:22
Alignment explanation
Indices: 1146802--1146854 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1146792 GAGATAGACG
*
1146802 GATTTCGCCGGAGATGAGGATT
1 GATTTCGCCGGAGATGAGGATA
* *
1146824 GATTTCGTCGGAGATGGGGATA
1 GATTTCGCCGGAGATGAGGATA
*
1146846 GATGTCGCC
1 GATTTCGCC
1146855 TTAGAGAGTG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.15, G:0.38, T:0.26
Consensus pattern (22 bp):
GATTTCGCCGGAGATGAGGATA
Found at i:1147033 original size:20 final size:20
Alignment explanation
Indices: 1147010--1147156 Score: 213
Period size: 20 Copynumber: 7.3 Consensus size: 20
1147000 GAAAATCGTA
*
1147010 TTGCGATAGTCAGCATCGCG
1 TTGCGATAGTCAGAATCGCG
*
1147030 TTGCGATAGTCAGCATCGCG
1 TTGCGATAGTCAGAATCGCG
*
1147050 CTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
1147070 TTGCGATAGTTAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
1147090 TTGCGATAGTCAGAATTGCG
1 TTGCGATAGTCAGAATCGCG
*
1147110 TTGCGATAGTCAGAATTGCG
1 TTGCGATAGTCAGAATCGCG
* *
1147130 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCG
1147150 TTGCGAT
1 TTGCGAT
1147157 TTACATATTC
Statistics
Matches: 116, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 116 1.00
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.29
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:1147189 original size:21 final size:21
Alignment explanation
Indices: 1147143--1147211 Score: 77
Period size: 21 Copynumber: 3.3 Consensus size: 21
1147133 CGATAGTCAT
** *
1147143 AATCGCATTGCG-ATTTACAT
1 AATCGCATTGCGAATTTGGAA
*
1147163 ATTCGCATTGCGAATTTGGAA
1 AATCGCATTGCGAATTTGGAA
**
1147184 AATCGCAACGCGAATTTGGAA
1 AATCGCATTGCGAATTTGGAA
1147205 AATCGCA
1 AATCGCA
1147212 ATGCAATAGT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 11 0.27
21 30 0.73
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (21 bp):
AATCGCATTGCGAATTTGGAA
Found at i:1147212 original size:21 final size:21
Alignment explanation
Indices: 1147172--1147212 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1147162 TATTCGCATT
1147172 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTGGAAAATCGCAAC
1147193 GCGAATTTGGAAAATCGCAA
1 GCGAATTTGGAAAATCGCAA
1147213 TGCAATAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATTTGGAAAATCGCAAC
Found at i:1160389 original size:24 final size:23
Alignment explanation
Indices: 1160342--1160442 Score: 88
Period size: 21 Copynumber: 4.5 Consensus size: 23
1160332 TTGTGCATAA
* *
1160342 TGCATCGATACA--CTATGAAGG
1 TGCATCGATGCATCCTATGAATG
1160363 TGCATCGATGCATTCCTATGAATG
1 TGCATCGATGCA-TCCTATGAATG
*
1160387 TGCATCGATACAT-C-ATGAA-G
1 TGCATCGATGCATCCTATGAATG
* *
1160407 ATGCACCGATGCACGCCT-TGAATG
1 -TGCATCGATGCA-TCCTATGAATG
1160431 TGCATCGATGCA
1 TGCATCGATGCA
1160443 CAGAGCCATG
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
20 1 0.02
21 26 0.40
22 1 0.02
23 17 0.26
24 20 0.31
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (23 bp):
TGCATCGATGCATCCTATGAATG
Found at i:1160406 original size:45 final size:44
Alignment explanation
Indices: 1160342--1160439 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 44
1160332 TTGTGCATAA
* * **
1160342 TGCATCGATACACTATGAAGGTGCATCGATGCATTCCTATGAATG
1 TGCATCGATACACTATGAAGATGCACCGATGCACGCCT-TGAATG
1160387 TGCATCGATACA-TCATGAAGATGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACT-ATGAAGATGCACCGATGCACGCCTTGAATG
1160431 TGCATCGAT
1 TGCATCGAT
1160440 GCACAGAGCC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
44 16 0.33
45 32 0.67
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (44 bp):
TGCATCGATACACTATGAAGATGCACCGATGCACGCCTTGAATG
Found at i:1163206 original size:64 final size:64
Alignment explanation
Indices: 1163085--1163217 Score: 146
Period size: 64 Copynumber: 2.1 Consensus size: 64
1163075 TTGTGTACCA
* * * **
1163085 ATGCACATACCATGCATCGATGCACTCCATATATATTAAAACATCGAATTAATTTTATGCA-CTG
1 ATGCACAAACCATGCATCGATGAACTCCAGATATATTAAAACATCGAAGCAATTTTATGCATC-G
* * *
1163149 ATGCACAAACCATGCATCGATGAAC-CCAGGCTTTTTTAAAACATCGAAGC-ATATTTATGCATC
1 ATGCACAAACCATGCATCGATGAACTCCA-GATATATTAAAACATCGAAGCAAT-TTTATGCATC
1163212 G
64 G
1163213 ATGCA
1 ATGCA
1163218 ATATCAGTGT
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
63 5 0.09
64 52 0.90
65 1 0.02
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.29
Consensus pattern (64 bp):
ATGCACAAACCATGCATCGATGAACTCCAGATATATTAAAACATCGAAGCAATTTTATGCATCG
Found at i:1164494 original size:22 final size:22
Alignment explanation
Indices: 1164467--1164508 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
1164457 AAACAATTCA
1164467 GGGGGGAATCGGTACCCTCTTG
1 GGGGGGAATCGGTACCCTCTTG
*
1164489 GGGGGGAATCGGTTCCCTCT
1 GGGGGGAATCGGTACCCTCT
1164509 GAGCAATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.12, C:0.24, G:0.40, T:0.24
Consensus pattern (22 bp):
GGGGGGAATCGGTACCCTCTTG
Found at i:1166682 original size:3 final size:3
Alignment explanation
Indices: 1166674--1166735 Score: 72
Period size: 3 Copynumber: 20.0 Consensus size: 3
1166664 TTTTATTTAT
* *
1166674 TTA TTA TTA TTA TTTA TTA TTA TTA CTA TTA TTA ATA TTA TTA TTTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
1166721 TTA TTAA TT- TTA TTA
1 TTA TT-A TTA TTA TTA
1166736 CAGGCCCAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
2 2 0.04
3 40 0.78
4 9 0.18
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1166714 original size:28 final size:28
Alignment explanation
Indices: 1166666--1166735 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
1166656 ACATTTGTTT
* *
1166666 TTATTTAT-TTATTATTATTATTTA-TTA
1 TTATTAATATTATTAATATTA-TTATTTA
*
1166693 TTATTACTATTATTAATATTATTATTTA
1 TTATTAATATTATTAATATTATTATTTA
*
1166721 TTATTAATTTTATTA
1 TTATTAATATTATTA
1166736 CAGGCCCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
27 9 0.25
28 27 0.75
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (28 bp):
TTATTAATATTATTAATATTATTATTTA
Found at i:1166735 original size:31 final size:31
Alignment explanation
Indices: 1166664--1166735 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
1166654 TTACATTTGT
*
1166664 TTTTATTTATTTATTATTATTATTTATTATTA
1 TTTTA-TTATTTAATATTATTATTTATTATTA
*
1166696 TTACTATTA-TTAATATTATTATTTATTATTAA
1 TT-TTATTATTTAATATTATTATTTATTATT-A
1166728 TTTTATTA
1 TTTTATTA
1166736 CAGGCCCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 25 0.71
32 8 0.23
33 2 0.06
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (31 bp):
TTTTATTATTTAATATTATTATTTATTATTA
Found at i:1168271 original size:20 final size:20
Alignment explanation
Indices: 1168246--1168288 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1168236 CTATTTTATA
1168246 AATTATATATTAATTGTTTT
1 AATTATATATTAATTGTTTT
* * *
1168266 AATTATTTATTTATTTTTTT
1 AATTATATATTAATTGTTTT
1168286 AAT
1 AAT
1168289 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTATATATTAATTGTTTT
Found at i:1168386 original size:29 final size:29
Alignment explanation
Indices: 1168344--1168400 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1168334 ATATTTCTAA
1168344 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTT-TTTCATAAATATAT
* *
1168373 ATAAATTAATATTTTTTTCATAATTATA
1 ATAAATAAATATTTTTTTCATAAATATA
1168401 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTTTTCATAAATATAT
Found at i:1175986 original size:24 final size:24
Alignment explanation
Indices: 1175959--1176031 Score: 146
Period size: 24 Copynumber: 3.0 Consensus size: 24
1175949 ATGAAAACTT
1175959 TTTGTTATCTTGTAAAGGAAATTA
1 TTTGTTATCTTGTAAAGGAAATTA
1175983 TTTGTTATCTTGTAAAGGAAATTA
1 TTTGTTATCTTGTAAAGGAAATTA
1176007 TTTGTTATCTTGTAAAGGAAATTA
1 TTTGTTATCTTGTAAAGGAAATTA
1176031 T
1 T
1176032 GTTAAGTTCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 49 1.00
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (24 bp):
TTTGTTATCTTGTAAAGGAAATTA
Found at i:1179656 original size:16 final size:15
Alignment explanation
Indices: 1179635--1179685 Score: 54
Period size: 16 Copynumber: 3.5 Consensus size: 15
1179625 TATTATGCTT
1179635 GAAGAAAAAATGAAAA
1 GAAGAAAAAA-GAAAA
*
1179651 GAAGAAAAGA-AAAA
1 GAAGAAAAAAGAAAA
*
1179665 G-A-AAAAAAGAGAA
1 GAAGAAAAAAGAAAA
1179678 GAAGAAAA
1 GAAGAAAA
1179686 CAGGGGAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
12 5 0.17
13 5 0.17
14 6 0.21
15 4 0.14
16 9 0.31
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (15 bp):
GAAGAAAAAAGAAAA
Found at i:1179664 original size:14 final size:13
Alignment explanation
Indices: 1179636--1179685 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1179626 ATTATGCTTG
1179636 AAGAA-AAAATGAA
1 AAGAAGAAAA-GAA
1179649 AAGAAGAAAAGAAA
1 AAGAAGAAAAG-AA
* *
1179663 AAGAAAAAAAGAG
1 AAGAAGAAAAGAA
1179676 AAGAAGAAAA
1 AAGAAGAAAA
1179686 CAGGGGAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
13 16 0.50
14 16 0.50
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (13 bp):
AAGAAGAAAAGAA
Found at i:1179668 original size:19 final size:20
Alignment explanation
Indices: 1179640--1179680 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1179630 TGCTTGAAGA
*
1179640 AAAAATGAAAAGAAGAAAAG
1 AAAAATGAAAAAAAGAAAAG
*
1179660 AAAAA-GAAAAAAAGAGAAG
1 AAAAATGAAAAAAAGAAAAG
1179679 AA
1 AA
1179681 GAAAACAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (20 bp):
AAAAATGAAAAAAAGAAAAG
Found at i:1180639 original size:114 final size:114
Alignment explanation
Indices: 1180434--1180770 Score: 611
Period size: 114 Copynumber: 3.0 Consensus size: 114
1180424 TGCCACGTTA
*
1180434 TCATGGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
*
1180499 TTTGGTATGAACCCCAGAACCAATCATAAGATTTGAAAGATGAATTTGC
66 TTTGGTATGAACCCCAGAACCAATCATTAGATTTGAAAGATGAATTTGC
*
1180548 TCATAGTAGAAATAAGGAGATCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* *
1180613 TTTGGTATGAACTCCAAAACCAATCATTAGATTTGAAAGATGAATTTGC
66 TTTGGTATGAACCCCAGAACCAATCATTAGATTTGAAAGATGAATTTGC
1180662 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
1 TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
* *
1180727 TTTGGTAGGAACCCCAGAACCAATCATTAGAATTGAAAGATGAA
66 TTTGGTATGAACCCCAGAACCAATCATTAGATTTGAAAGATGAA
1180771 CTGCATGATT
Statistics
Matches: 213, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
114 213 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG
TTTGGTATGAACCCCAGAACCAATCATTAGATTTGAAAGATGAATTTGC
Found at i:1181656 original size:113 final size:113
Alignment explanation
Indices: 1181458--1181849 Score: 570
Period size: 113 Copynumber: 3.5 Consensus size: 113
1181448 GCAAAGATTT
* ** ** * *
1181458 AAATCCATCATTTAATGGATCAACATTT-TCAGTCAGAGTTCATAATGAGATGAACTCATCTGAA
1 AAATCCATCACTCGATGGATCAACATTTCT-AGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
*
1181522 GAAGGAATAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
1181571 AAATCCATCACTCGATGGATCAACATTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTCGATGGATCAACATTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
*
1181636 AATGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
* * *
1181684 AAATCCATCACTCGATGGATCAGCAGTTCAAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATCCATCACTCGATGGATCAACATTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * * *
1181749 AAGGAAGAAGAAGTTTATAATGAGAAGAACTTGTTCAACTTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
* * * * *
1181797 GAATTCATCATTCGATGGATCATCATTTCCAGAGAAAGTTCATAATGAGAAGA
1 AAATCCATCACTCGATGGATCAACATTTCTAGAGAAAGTTCATAATGAGAAGA
1181850 GCTTGTTCAA
Statistics
Matches: 254, Mismatches: 24, Indels: 2
0.91 0.09 0.01
Matches are distributed among these distances:
113 253 1.00
114 1 0.00
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
AAATCCATCACTCGATGGATCAACATTTCTAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTCAACCTTTTGCTC
Found at i:1182111 original size:112 final size:110
Alignment explanation
Indices: 1181899--1182214 Score: 381
Period size: 112 Copynumber: 2.8 Consensus size: 110
1181889 ATATATCATC
* * *
1181899 ATCAGCTTTTCCAGA-AGGAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAAAAAGTTCATAA
1 ATCAACTTGTCCAGAGA-GAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAAGTTCATAA
* * *
1181963 TGAGAAGAGCTTGTTCAACCTTTTGTTTAAATTCATCATTTGATGG
65 TGAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTCGATGG
*
1182009 ATCAACATTGT-CAG-GTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAGAAA-TTT
1 ATCAAC-TTGTCCAGAG-AGAGTTCATAATGAGAAGAACT--T-ATCTGAAGAAGAAGAAAGTTC
*
1182071 ATAATGAGAAGAATTTGTTCAA-CTTTCTGTTTAAATTCATCACTCGATGG
61 ATAATGAGAAGAACTTGTTCAACCTTT-TGTTTAAATTCATCACTCGATGG
* * *
1182121 ATCAACTTTTCCAGAGAAAATTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGAAGTTC
1 ATCAACTTGTCCAGAGAGAGTTCATAATGAGAAGAACTTATCT---GAAGAAGAAG-A-AAGTTC
*
1182186 ATAATGAGAAGAGCTTGTTCAACCTTTTG
61 ATAATGAGAAGAACTTGTTCAACCTTTTG
1182215 CATAACTCTA
Statistics
Matches: 176, Mismatches: 14, Indels: 27
0.81 0.06 0.12
Matches are distributed among these distances:
109 4 0.02
110 30 0.17
111 11 0.06
112 83 0.47
113 18 0.10
114 2 0.01
115 24 0.14
116 4 0.02
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (110 bp):
ATCAACTTGTCCAGAGAGAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAAGTTCATAAT
GAGAAGAACTTGTTCAACCTTTTGTTTAAATTCATCACTCGATGG
Found at i:1182554 original size:3 final size:3
Alignment explanation
Indices: 1182548--1182609 Score: 63
Period size: 3 Copynumber: 20.0 Consensus size: 3
1182538 ATTTGTTTTT
* * *
1182548 TTA TTA TTA TTA TTTA TTA TTA TTA CTA TTA TTA ATA TTT TTA TTTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
1182595 TTA TTA CTT- TTA TTA
1 TTA TTA -TTA TTA TTA
1182610 CAGACCCAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 2 0.04
3 39 0.80
4 8 0.16
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1182595 original size:28 final size:28
Alignment explanation
Indices: 1182548--1182609 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1182538 ATTTGTTTTT
*
1182548 TTATTATTATTATTTATTATTATTACTA
1 TTATTAATATTATTTATTATTATTACTA
*
1182576 TTATTAATATT-TTTATTTATTATTACTT
1 TTATTAATATTATTTA-TTATTATTACTA
1182604 TTATTA
1 TTATTA
1182610 CAGACCCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 4 0.13
28 27 0.87
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (28 bp):
TTATTAATATTATTTATTATTATTACTA
Found at i:1183861 original size:3 final size:3
Alignment explanation
Indices: 1183853--1183882 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1183843 TTTACTTTTA
*
1183853 ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1183883 TAACCATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:1183905 original size:24 final size:23
Alignment explanation
Indices: 1183873--1183931 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 23
1183863 CTATTATTAT
*
1183873 TATTATTATTTAAC-CATAAATATA
1 TATT-TTATTTAACAAAT-AATATA
* *
1183897 TATATTTATATAACAAATAATATG
1 TAT-TTTATTTAACAAATAATATA
1183921 TATTTTATTTA
1 TATTTTATTTA
1183932 TTAAAATCTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
23 7 0.24
24 19 0.66
25 3 0.10
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (23 bp):
TATTTTATTTAACAAATAATATA
Found at i:1184100 original size:20 final size:20
Alignment explanation
Indices: 1184075--1184117 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1184065 CTATTTTATA
1184075 AATTATATATTAATTGTTTT
1 AATTATATATTAATTGTTTT
* * *
1184095 AATTATTTATTTATTTTTTT
1 AATTATATATTAATTGTTTT
1184115 AAT
1 AAT
1184118 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTATATATTAATTGTTTT
Found at i:1184206 original size:29 final size:29
Alignment explanation
Indices: 1184173--1184229 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
1184163 ATATTTCTAA
1184173 ATAAATAAATATTTTATTT-ATAAATATAT
1 ATAAATAAATATTTT-TTTCATAAATATAT
* *
1184202 ATAAATTAATATTTTTTTCATAATTATA
1 ATAAATAAATATTTTTTTCATAAATATA
1184230 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (29 bp):
ATAAATAAATATTTTTTTCATAAATATAT
Found at i:1185187 original size:20 final size:21
Alignment explanation
Indices: 1185133--1185195 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1185123 GATTCCCCTG
1185133 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1185157 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1185177 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1185196 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1194732 original size:13 final size:13
Alignment explanation
Indices: 1194714--1194758 Score: 58
Period size: 13 Copynumber: 3.6 Consensus size: 13
1194704 TAAGTCGAAG
1194714 AAAGAAAAAAGAA
1 AAAGAAAAAAGAA
*
1194727 AAAGAAAAAGGAA
1 AAAGAAAAAAGAA
*
1194740 CAA-AAAAAAG-A
1 AAAGAAAAAAGAA
1194751 AAAGAAAA
1 AAAGAAAA
1194759 TAAGGTGGGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 3 0.11
12 10 0.37
13 14 0.52
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAAGAA
Found at i:1195678 original size:110 final size:110
Alignment explanation
Indices: 1195481--1195955 Score: 642
Period size: 110 Copynumber: 4.4 Consensus size: 110
1195471 GGTTTTAGCT
* * *
1195481 AGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
* * *
1195546 CAAAGAGGCGACTGACTATCAACAAACAACTTTTCAGTTTCATTC
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
*
1195591 AGAGTCAATTTCAACTTCACAGCGAATGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
*
1195656 CGAAGGGGTGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
* *
1195701 AGAGTCAATTTCAACTTCAC-GTCGAAAGATATTAGACTCGAAACAACACAAGCTCAACTTCACA
1 AGAGTCAATTTCAACTTCACAG-CGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACA
* * * *
1195765 GCGAATGGGTGATTGACTGTCAACAAACAACTTTTCAGTTTCATGC
65 GCGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
* * * *
1195811 AAAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGCTCAACTTCGCAG
1 AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
* * * *
1195876 CGAATGGGCG-GTGGCTGTCAACAAACAA-TTTCCTAG-TTC---C
66 CGAAGGGGCGACTGACTGTCAACAAACAACTTTTC-AGTTTCATTC
* * *
1195916 AGAGCCAATTTCAACTTCACGGC-AGAGGATATTGGACTCG
1 AGAGTCAATTTCAACTTCACAGCGA-AGGATATTAGACTCG
1195956 GAACAATACA
Statistics
Matches: 334, Mismatches: 27, Indels: 13
0.89 0.07 0.03
Matches are distributed among these distances:
104 1 0.00
105 35 0.10
108 7 0.02
109 19 0.06
110 272 0.81
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (110 bp):
AGAGTCAATTTCAACTTCACAGCGAAGGATATTAGACTCGAGACAACACAAGCTCAACTTCACAG
CGAAGGGGCGACTGACTGTCAACAAACAACTTTTCAGTTTCATTC
Found at i:1196750 original size:2 final size:2
Alignment explanation
Indices: 1196738--1196805 Score: 99
Period size: 2 Copynumber: 36.0 Consensus size: 2
1196728 CGAAATAAAC
1196738 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
1196777 AT AT AT AT AT AT AT AT AT -T AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1196806 TATTATTATT
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
1 4 0.07
2 56 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1196778 original size:30 final size:32
Alignment explanation
Indices: 1196738--1196808 Score: 110
Period size: 30 Copynumber: 2.3 Consensus size: 32
1196728 CGAAATAAAC
*
1196738 ATATAATATATATATATATATATATA-TAT-T
1 ATATATTATATATATATATATATATATTATAT
1196768 ATATATTATATATATATATATATATATTATAT
1 ATATATTATATATATATATATATATATTATAT
*
1196800 AAATATTAT
1 ATATATTAT
1196809 TATTATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 25 0.68
31 3 0.08
32 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATATATTATATATATATATATATATATTATAT
Found at i:1196799 original size:28 final size:28
Alignment explanation
Indices: 1196746--1196800 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1196736 ACATATAATA
1196746 TATATATATATATATATATATTATATAT
1 TATATATATATATATATATATTATATAT
1196774 TATATATATATATATATATATTATATA
1 TATATATATATATATATATATTATATA
1196801 AATATTATTA
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:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TATATATATATATATATATATTATATAT
Found at i:1197860 original size:10 final size:10
Alignment explanation
Indices: 1197845--1197914 Score: 56
Period size: 10 Copynumber: 6.7 Consensus size: 10
1197835 TTTTAATTTA
1197845 ATTATTTTTT
1 ATTATTTTTT
1197855 ATTA-TTTTT
1 ATTATTTTTT
1197864 ATTTATTTATTT
1 A-TTATTT-TTT
1197876 ATTTATTCTTATT
1 A-TTATT-TT-TT
*
1197889 A-TATTTCTT
1 ATTATTTTTT
1197898 ATTATTTTGTT
1 ATTATTTT-TT
1197909 -TTATTT
1 ATTATTT
1197915 ATACGATATT
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
9 9 0.18
10 19 0.37
11 8 0.16
12 11 0.22
13 4 0.08
ACGTcount: A:0.21, C:0.03, G:0.01, T:0.74
Consensus pattern (10 bp):
ATTATTTTTT
Found at i:1197867 original size:24 final size:25
Alignment explanation
Indices: 1197835--1197882 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
1197825 TTTGTTTCCC
1197835 TTTTAATTTAATTATTT-TTTATTA
1 TTTTAATTTAATTATTTATTTATTA
* *
1197859 TTTTTATTTATTTATTTATTTATT
1 TTTTAATTTAATTATTTATTTATT
1197883 CTTATTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (25 bp):
TTTTAATTTAATTATTTATTTATTA
Found at i:1197870 original size:4 final size:4
Alignment explanation
Indices: 1197840--1197882 Score: 52
Period size: 4 Copynumber: 10.8 Consensus size: 4
1197830 TTCCCTTTTA
* *
1197840 ATTT AATT ATTT -TTT ATTAT TTTT ATTT ATTT ATTT ATTT ATT
1 ATTT ATTT ATTT ATTT ATT-T ATTT ATTT ATTT ATTT ATTT ATT
1197883 CTTATTATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
3 3 0.09
4 27 0.82
5 3 0.09
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:1197899 original size:22 final size:21
Alignment explanation
Indices: 1197846--1197900 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
1197836 TTTAATTTAA
*
1197846 TTATTTTTTA-TTATTTTTAT
1 TTATTTTTTATTTATTCTTAT
1197866 TTATTTATTTATTTATTCTTAT
1 TTATTT-TTTATTTATTCTTAT
*
1197888 TATATTTCTTATT
1 T-TATTTTTTATT
1197901 ATTTTGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 6 0.20
21 4 0.13
22 15 0.50
23 5 0.17
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTTTTATTTATTCTTAT
Found at i:1197902 original size:15 final size:14
Alignment explanation
Indices: 1197845--1197904 Score: 65
Period size: 12 Copynumber: 4.5 Consensus size: 14
1197835 TTTTAATTTA
1197845 ATTATTT-TTTATT
1 ATTATTTATTTATT
1197858 ATT-TTTATTTA-T
1 ATTATTTATTTATT
1197870 -TTATTTATTTATT
1 ATTATTTATTTATT
* *
1197883 CTTATTATATTTCTT
1 ATTATT-TATTTATT
1197898 ATTATTT
1 ATTATTT
1197905 TGTTTTATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 2 0.05
12 12 0.30
13 8 0.20
14 6 0.15
15 12 0.30
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTATTTATTTATT
Found at i:1198388 original size:19 final size:19
Alignment explanation
Indices: 1198344--1198380 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1198334 TTGGTTTTTC
*
1198344 ATATTTTATTATTTTATTA
1 ATATTTTATTATTCTATTA
*
1198363 CTATTTTATTATTCTATT
1 ATATTTTATTATTCTATT
1198381 TAATTTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (19 bp):
ATATTTTATTATTCTATTA
Found at i:1201050 original size:77 final size:77
Alignment explanation
Indices: 1200932--1201224 Score: 338
Period size: 77 Copynumber: 3.8 Consensus size: 77
1200922 TGTGCCTAAA
* * *
1200932 AATGTCATGGTTCACTAAAAAATAGGTTGTGATCTGAAATGTTAACATTTTTATTAATAAAATGG
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATCTGGAATGTTAATATTTTTATTAATAAAATGG
* *
1200997 GTTGTGTCC-AAG
66 ATTGCG-CCAAAG
* ** ** * *
1201009 AATATCATGGTTCACTAAGAAATAAATTGTTTTATGGAATGTTAATATTTTTATTAATAAATTGG
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATCTGGAATGTTAATATTTTTATTAATAAAATGG
*
1201074 ATTGCGCCTAAG
66 ATTGCGCCAAAG
* * ** *
1201086 AATGTCATTGTTCTCTAAGAAATAGGTTACGATCTGGAACGTTAATATTTTTATTAATAAAATGG
1 AATGTCATGGTTCACTAAGAAATAGGTTGTGATCTGGAATGTTAATATTTTTATTAATAAAATGG
*
1201151 ATTGCGCCAAAA
66 ATTGCGCCAAAG
* * * **
1201163 AATGTTATGGTTCACTAAGAAAGTATGATGCAATCTGGAATGTTAATATTTTTATT-ATAAAA
1 AATGTCATGGTTCACTAAGAAA-TAGGTTGTGATCTGGAATGTTAATATTTTTATTAATAAAA
1201225 AAATTTGAAA
Statistics
Matches: 180, Mismatches: 34, Indels: 4
0.83 0.16 0.02
Matches are distributed among these distances:
76 2 0.01
77 150 0.83
78 28 0.16
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.38
Consensus pattern (77 bp):
AATGTCATGGTTCACTAAGAAATAGGTTGTGATCTGGAATGTTAATATTTTTATTAATAAAATGG
ATTGCGCCAAAG
Found at i:1201223 original size:154 final size:154
Alignment explanation
Indices: 1200925--1201223 Score: 379
Period size: 154 Copynumber: 1.9 Consensus size: 154
1200915 ATACAGTTGT
** *
1200925 GCCTAAAAATGTCATGGTTCACTAAAAAATAGGTTGTGATCTGAAATGTTAACATTTTTATTAAT
1 GCCTAAAAATGTCATGGTTCACTAAAAAATAGGTTACGATCTGAAACGTTAACATTTTTATTAAT
* * * ***
1200990 AAAATGGGTTGTGTCCAAGAATATCATGGTTCACTAAGAAATAAATTGTTTTATGGAATGTTAAT
66 AAAATGGATTGCGTCCAAAAATATCATGGTTCACTAAGAAATAAATTGCAATATGGAATGTTAAT
1201055 ATTTTTATTAATAAATTGGATTGC
131 ATTTTTATTAATAAATTGGATTGC
* * * * * *
1201079 GCCTAAGAATGTCATTGTTCTCTAAGAAATAGGTTACGATCTGGAACGTTAATATTTTTATTAAT
1 GCCTAAAAATGTCATGGTTCACTAAAAAATAGGTTACGATCTGAAACGTTAACATTTTTATTAAT
* * * *
1201144 AAAATGGATTGCG-CCAAAAAATGTTATGGTTCACTAAGAAAGTATGA-TGCAATCTGGAATGTT
66 AAAATGGATTGCGTCC-AAAAATATCATGGTTCACTAAGAAA-TA-AATTGCAATATGGAATGTT
1201207 AATATTTTTATT-ATAAA
128 AATATTTTTATTAATAAA
1201224 AAAATTTGAA
Statistics
Matches: 123, Mismatches: 19, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
153 2 0.02
154 94 0.76
155 26 0.21
156 1 0.01
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.37
Consensus pattern (154 bp):
GCCTAAAAATGTCATGGTTCACTAAAAAATAGGTTACGATCTGAAACGTTAACATTTTTATTAAT
AAAATGGATTGCGTCCAAAAATATCATGGTTCACTAAGAAATAAATTGCAATATGGAATGTTAAT
ATTTTTATTAATAAATTGGATTGC
Found at i:1201580 original size:99 final size:99
Alignment explanation
Indices: 1201464--1201936 Score: 336
Period size: 98 Copynumber: 4.8 Consensus size: 99
1201454 TTTTGTTATG
* * * *
1201464 CTCATGATAAAGTAGTAGGTAACGTTTTTTTAATGTCAACTGTTTAATTTACAAATATCAAATTG
1 CTCATGATAACGTAGTAGGTAACGTTTTTTTAATGTCAACTGTTTAAATTATAAGTATCAAATTG
* *
1201529 TTTATATGATGCATAAGTAAGATAAAACATGTTT
66 TTTATATTATGCAAAAGTAAGATAAAACATGTTT
* * * * ** * * **
1201563 CTCATGATAACGAAGTAGTTAGCGCATTTTTT-ATGTCAA-TCATTAAGTTATAAGTATAAAACC
1 CTCATGATAACGTAGTAGGTAACG-TTTTTTTAATGTCAACTGTTTAAATTATAAGTATCAAATT
*
1201626 GTTTATATTATGCAAAAAGAAAGATAAAACAT-TTT
65 GTTTATATTATGC-AAAAGTAAGATAAAACATGTTT
* * * *
1201661 GCTCATTATAACGTA-TCAGGTAGCACCTTTTTTTAATGTCAGCCGTTTAAATTATAAGTA-CGA
1 -CTCATGATAACGTAGT-AGGTA--ACGTTTTTTTAATGTCAACTGTTTAAATTATAAGTATC-A
* * * *
1201724 AATTGTTTATATTATGTAAAAGTAAGACAAAATAAGTTT
61 AATTGTTTATATTATGCAAAAGTAAGATAAAACATGTTT
* * * * * ** **
1201763 ATCATGATAACGTAGTATGTAGCGTTTTTTT-ATGTTAA-TAGTTTAAGTTATAAGTATGTGACC
1 CTCATGATAACGTAGTAGGTAACGTTTTTTTAATGTCAACT-GTTTAAATTATAAGTAT-CAAAT
* * * * *
1201826 T-ATTATATTATGAAAAAGTAAGACAAAGCA-GATTG
64 TGTTTATATTATGCAAAAGTAAGATAAAACATG-TTT
** * * * * * *
1201861 CTCATGATAATATACTAGGTAACAAATTTTTTT-ATGTCAACCGTTTAAGTTATAAGTATGAAAC
1 CTCATGATAACGTAGTAGGTAAC--GTTTTTTTAATGTCAACTGTTTAAATTATAAGTATCAAAT
*
1201925 TATTTATATTAT
64 TGTTTATATTAT
1201937 TAAATATTAA
Statistics
Matches: 289, Mismatches: 66, Indels: 37
0.74 0.17 0.09
Matches are distributed among these distances:
97 1 0.00
98 96 0.33
99 72 0.25
100 51 0.18
101 37 0.13
102 32 0.11
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (99 bp):
CTCATGATAACGTAGTAGGTAACGTTTTTTTAATGTCAACTGTTTAAATTATAAGTATCAAATTG
TTTATATTATGCAAAAGTAAGATAAAACATGTTT
Found at i:1201834 original size:200 final size:199
Alignment explanation
Indices: 1201462--1201940 Score: 496
Period size: 200 Copynumber: 2.4 Consensus size: 199
1201452 TATTTTGTTA
* * * * * *
1201462 TGCTCATGATAA-AGTAGTAGGTAAC--GTTTTTTTAATGTCAACTGTTTAATTTACAAATATC-
1 TGCTCATGATAATA-TACTAGGTAACAAATTTTTTTAATGTCAACCGTTTAAATTATAAGTA-CG
* * * * * *
1201523 AAATTGTTTATATGATGCATAAGTAAGATAAAACATGTTTCTCATGATAACGAAGTAGTTAGCGC
64 AAATTGTTTATATTATGTAAAAGTAAGACAAAACAAGTTTATCATGATAACGAAGTAGTTAGCGC
*
1201588 ATTTTTTATGTCAATCATTAAGTTATAAGTATAAAACCGTTTATATTATGCAAAAAGAAAGATAA
129 ATTTTTTATGTCAATCATTAAGTTATAAGTATAAAACCGTTTATATTATG-AAAAAGAAAGACAA
**
1201653 AACATTT
193 AACAGAT
* * ** *
1201660 TGCTCATTATAACGTAT-C-AGGTAGCACCTTTTTTTAATGTCAGCCGTTTAAATTATAAGTACG
1 TGCTCATGATAA--TATACTAGGTAACAAATTTTTTTAATGTCAACCGTTTAAATTATAAGTACG
* *
1201723 AAATTGTTTATATTATGTAAAAGTAAGACAAAATAAGTTTATCATGATAACGTAGTA-TGTAGCG
64 AAATTGTTTATATTATGTAAAAGTAAGACAAAACAAGTTTATCATGATAACGAAGTAGT-TAGCG
* * *** *
1201787 -TTTTTTTATGTTAAT-AGTTTAAGTTATAAGTATGTGACC-TATTATATTATGAAAAAGTAAGA
128 CATTTTTTATGTCAATCA--TTAAGTTATAAGTATAAAACCGT-TTATATTATGAAAAAGAAAGA
*
1201849 CAAAGCAGAT
190 CAAAACAGAT
* *
1201859 TGCTCATGATAATATACTAGGTAACAAATTTTTTT-ATGTCAACCGTTTAAGTTATAAGTATGAA
1 TGCTCATGATAATATACTAGGTAACAAATTTTTTTAATGTCAACCGTTTAAATTATAAGTACGAA
* *
1201923 ACTATTTATATTAT-TAAA
66 ATTGTTTATATTATGTAAA
1201941 TATTAATACA
Statistics
Matches: 233, Mismatches: 36, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
197 7 0.03
198 57 0.24
199 57 0.24
200 111 0.48
201 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (199 bp):
TGCTCATGATAATATACTAGGTAACAAATTTTTTTAATGTCAACCGTTTAAATTATAAGTACGAA
ATTGTTTATATTATGTAAAAGTAAGACAAAACAAGTTTATCATGATAACGAAGTAGTTAGCGCAT
TTTTTATGTCAATCATTAAGTTATAAGTATAAAACCGTTTATATTATGAAAAAGAAAGACAAAAC
AGAT
Found at i:1202424 original size:77 final size:77
Alignment explanation
Indices: 1202332--1202477 Score: 195
Period size: 77 Copynumber: 1.9 Consensus size: 77
1202322 TTCTTAGGCA
* * * * *
1202332 CAACCTATTTCATTAAAAAAAATATTACT-TTATAAATCGCAACATATTTTCTTAGTGAACCATT
1 CAACCTATTTCATTAAAAAAAATATTAATATTACAAATCACAACATA-TTTATTAGTGAACCATG
1202396 ACATTCTAGGGTG
65 ACATTCTAGGGTG
* * * *
1202409 CAACGTATTTTATTAATAAAAATATTAATATTACATATCACAACATATTTATTAGTGAACCATGA
1 CAACCTATTTCATTAAAAAAAATATTAATATTACAAATCACAACATATTTATTAGTGAACCATGA
1202474 CATT
66 CATT
1202478 ATTGGGTGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
77 45 0.76
78 14 0.24
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (77 bp):
CAACCTATTTCATTAAAAAAAATATTAATATTACAAATCACAACATATTTATTAGTGAACCATGA
CATTCTAGGGTG
Found at i:1202485 original size:77 final size:77
Alignment explanation
Indices: 1202332--1202499 Score: 194
Period size: 77 Copynumber: 2.2 Consensus size: 77
1202322 TTCTTAGGCA
* * * * *
1202332 CAACCTATTTCATTAAAAAAAATATTACTTTATAAATCGCAACATATTTTCTTAGTGAACCATTA
1 CAACCTATTTCATTAAAAAAAATATTAATTTACAAATCACAACATATTTTATTAGTGAACCATGA
*
1202397 CATTCTAGGGTG
66 CATTATAGGGTG
* * * *
1202409 CAACGTATTTTATTAATAAAAATATTAATATTACATATCACAACATA-TTTATTAGTGAACCATG
1 CAACCTATTTCATTAAAAAAAATATTAAT-TTACAAATCACAACATATTTTATTAGTGAACCATG
*
1202473 ACATTATTGGGTG
65 ACATTATAGGGTG
* *
1202486 AAAACATATTTCAT
1 -CAACCTATTTCAT
1202500 ATATATATAT
Statistics
Matches: 75, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
77 51 0.68
78 24 0.32
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (77 bp):
CAACCTATTTCATTAAAAAAAATATTAATTTACAAATCACAACATATTTTATTAGTGAACCATGA
CATTATAGGGTG
Found at i:1202505 original size:2 final size:2
Alignment explanation
Indices: 1202498--1202543 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
1202488 AACATATTTC
1202498 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1202540 AT AT
1 AT AT
1202544 TCATAACATC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1203496 original size:14 final size:14
Alignment explanation
Indices: 1203479--1203521 Score: 86
Period size: 14 Copynumber: 3.1 Consensus size: 14
1203469 TGTTTTGCCC
1203479 CTAAAATTTTAATT
1 CTAAAATTTTAATT
1203493 CTAAAATTTTAATT
1 CTAAAATTTTAATT
1203507 CTAAAATTTTAATT
1 CTAAAATTTTAATT
1203521 C
1 C
1203522 GACACCTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (14 bp):
CTAAAATTTTAATT
Found at i:1204189 original size:4 final size:4
Alignment explanation
Indices: 1204180--1204208 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
1204170 CAGTATCCCC
1204180 TCTT TCTT TCTT TCTT TCTT TCTT T-TT TC
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TC
1204209 CGGGTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:1210891 original size:15 final size:15
Alignment explanation
Indices: 1210794--1210907 Score: 79
Period size: 15 Copynumber: 7.3 Consensus size: 15
1210784 ACATTAGATA
1210794 AAAAAAATAATAAAT
1 AAAAAAATAATAAAT
*
1210809 AAATAGTAATAAT-AAT
1 AAA-A-AAATAATAAAT
* *
1210825 AATAATAATAA-AATT
1 AA-AAAAATAATAAAT
**
1210840 AACTGAAATAATAAAT
1 AA-AAAAATAATAAAT
* **
1210856 AAAAAGATAGGAAAGT
1 AAAAAAATAATAAA-T
1210872 AAAAAAATGAATAAAT
1 AAAAAAAT-AATAAAT
*
1210888 AAAAAAATATTAAAT
1 AAAAAAATAATAAAT
1210903 AAAAA
1 AAAAA
1210908 CGAAAACAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
15 36 0.47
16 29 0.38
17 11 0.14
ACGTcount: A:0.70, C:0.01, G:0.06, T:0.23
Consensus pattern (15 bp):
AAAAAAATAATAAAT
Found at i:1211006 original size:33 final size:31
Alignment explanation
Indices: 1210958--1211041 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 31
1210948 AATAAGATAT
* * * *
1210958 AAAAAATAAATAAATAATAATAATGACGATGAA
1 AAAAAATTAA-AAATAAAAACAAT-ACGAAGAA
* *
1210991 AAAAATGTTAAAAATAAAAACAATATGAAGAA
1 AAAAA-ATTAAAAATAAAAACAATACGAAGAA
1211023 AAAAAATTAAAAATAAAAA
1 AAAAAATTAAAAATAAAAA
1211042 GCTTAACGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 13 0.30
32 11 0.26
33 16 0.37
34 3 0.07
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (31 bp):
AAAAAATTAAAAATAAAAACAATACGAAGAA
Found at i:1211182 original size:20 final size:22
Alignment explanation
Indices: 1211145--1211190 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
1211135 CTAAAATAAC
1211145 AAAACAAGAACTTAAAAGG-CT
1 AAAACAAGAACTTAAAAGGACT
* *
1211166 AAAAC-AGAATTTTAAAGGACT
1 AAAACAAGAACTTAAAAGGACT
1211187 AAAA
1 AAAA
1211191 TAACAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (22 bp):
AAAACAAGAACTTAAAAGGACT
Found at i:1212636 original size:37 final size:37
Alignment explanation
Indices: 1212586--1212738 Score: 116
Period size: 37 Copynumber: 4.4 Consensus size: 37
1212576 AAGATATCTG
*
1212586 TTGTTTCATGAGAAAC-GATCTCAAGGGAGAC-AAGATT
1 TTGTTTCAAGAGAAACAGATCTCAAGGGAGACGAA-A-T
*
1212623 TTGTTTCAAGAGAAACTG-TCTCAAGGGAGACGAAAT
1 TTGTTTCAAGAGAAACAGATCTCAAGGGAGACGAAAT
* *
1212659 TAGTTTCAA-AGAAACAGAT-TC-A---A-A-G-ATT
1 TTGTTTCAAGAGAAACAGATCTCAAGGGAGACGAAAT
* * * *
1212687 TTGTTTCAAGGGAAACTG-TCTCAAGAGAGACTAAAT
1 TTGTTTCAAGAGAAACAGATCTCAAGGGAGACGAAAT
*
1212723 TTGTTTCAAGAAAAAC
1 TTGTTTCAAGAGAAAC
1212739 TGCTTCAAAC
Statistics
Matches: 93, Mismatches: 11, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
28 11 0.12
29 9 0.10
30 2 0.02
31 1 0.01
33 1 0.01
34 2 0.02
35 9 0.10
36 26 0.28
37 29 0.31
38 3 0.03
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (37 bp):
TTGTTTCAAGAGAAACAGATCTCAAGGGAGACGAAAT
Found at i:1212723 original size:64 final size:65
Alignment explanation
Indices: 1212617--1212769 Score: 209
Period size: 64 Copynumber: 2.3 Consensus size: 65
1212607 CAAGGGAGAC
* * *
1212617 AAGATTTTGTTTCAAGAGAAACTGTCTCAAGGGAGACGAAATTAGTTTCAA-AGAAACAGATTCA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAAAAACAGATTCA
* * * *
1212681 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACTAAATTTGTTTCAAGAAAAACTGCTTCA
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAAAAACAGATTCA
*
1212746 AACATCTTGTGTTTCAAGGGAAAC
1 AAGAT-TT-TGTTTCAAGGGAAAC
1212770 GTTTTCAAAG
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
64 47 0.60
65 14 0.18
66 2 0.03
67 15 0.19
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (65 bp):
AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACGAAATTAGTTTCAAGAAAAACAGATTCA
Found at i:1212842 original size:36 final size:36
Alignment explanation
Indices: 1212787--1212953 Score: 147
Period size: 36 Copynumber: 4.8 Consensus size: 36
1212777 AAGTTTTATG
* *
1212787 TTTCAAGAGAAA-TCGTCTCAAGGGAGACAAAATTTA
1 TTTCAAGGGAAACT-GTCTCAAGAGAGACAAAATTTA
* *
1212823 TTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
* * *
1212859 TTTCAAGGGAAA-TGTTTTC-A-A-TG-C----TTATG
1 TTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT-TA
** *
1212888 TTTCAAGAAAAACTGTCTCAAGGGAGACAAAATTTA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
1212924 TTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTTCAAGGGAAACTGTCTCAAGAGAGACAA
1212954 TGGTGAGCAC
Statistics
Matches: 101, Mismatches: 18, Indels: 24
0.71 0.13 0.17
Matches are distributed among these distances:
28 2 0.02
29 13 0.13
30 3 0.03
32 2 0.02
33 2 0.02
34 1 0.01
35 2 0.02
36 73 0.72
37 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (36 bp):
TTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTA
Found at i:1212911 original size:101 final size:102
Alignment explanation
Indices: 1212757--1212953 Score: 326
Period size: 101 Copynumber: 1.9 Consensus size: 102
1212747 ACATCTTGTG
* *
1212757 TTTCAAGGGAAACGTTTTCAAAGTTTTATGTTTCAAGAGAAATCGTCTCAAGGGAGACAAAATTT
1 TTTCAAGGGAAACGTTTTCAAAGTCTTATGTTTCAAGAAAAATCGTCTCAAGGGAGACAAAATTT
1212822 ATTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
66 ATTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
* *
1212859 TTTCAAGGGAAATGTTTTCAATG-CTTATGTTTCAAGAAAAA-CTGTCTCAAGGGAGACAAAATT
1 TTTCAAGGGAAACGTTTTCAAAGTCTTATGTTTCAAGAAAAATC-GTCTCAAGGGAGACAAAATT
*
1212922 TATTTCAAGGGAAACTGTCTCAAGAGAGACAA
65 TATTTCAAGGGAAACTATCTCAAGAGAGACAA
1212954 TGGTGAGCAC
Statistics
Matches: 89, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
100 1 0.01
101 67 0.75
102 21 0.24
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (102 bp):
TTTCAAGGGAAACGTTTTCAAAGTCTTATGTTTCAAGAAAAATCGTCTCAAGGGAGACAAAATTT
ATTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCA
Found at i:1213263 original size:106 final size:106
Alignment explanation
Indices: 1213078--1214418 Score: 2101
Period size: 106 Copynumber: 12.6 Consensus size: 106
1213068 GTATTGCTCC
* * * * * *
1213078 GAGTCCAATATCCTTCGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1213143 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * * *
1213184 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTAGATCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1213249 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* *
1213290 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
1213355 CCAGTGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * *
1213396 GTGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGATCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
1213461 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * *
1213502 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTATGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1213567 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* *
1213608 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTATTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1213673 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * * * *
1213714 GAGTCCGATATCCTTCGTTATGAAGTTTTAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 GAGTCCAATATCCTTCGCTGTGAAG-TTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1213779 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
*
1213821 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1213886 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCAT-
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTC-TG
*
1213927 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1213992 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * *
1214033 GAGTCCAATACCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1214098 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * *
1214139 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
1214204 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * * * *
1214245 GAGTCCACTATCCTTCGCTGTGAAGTTGAAATTGGCTCT-AGAAGTGGAAAATTGTTTATTGACA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-AATTGGGAAGTTGTTTGTTGACA
*
1214309 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
* * * * * * *
1214351 GAGTTCAATTTTCTTCGCTGCGAAGTTGAAATAGACTCTGAATGAAATTGGAAAGTTGTTTGTTG
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC----TGAAATTGGGAAGTTGTTTGTTG
1214416 ACA
62 ACA
1214419 GACAACTTTT
Statistics
Matches: 1159, Mismatches: 67, Indels: 14
0.93 0.05 0.01
Matches are distributed among these distances:
105 2 0.00
106 1034 0.89
107 101 0.09
110 21 0.02
111 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTG
Found at i:1218340 original size:3 final size:3
Alignment explanation
Indices: 1218278--1218322 Score: 54
Period size: 3 Copynumber: 14.3 Consensus size: 3
1218268 AAAAGATTAG
* *
1218278 ATA AAA ATA ATA ATAA ATAA ATA GTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA AT-A AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
1218323 AATTAACTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
3 30 0.81
4 7 0.19
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:1218379 original size:16 final size:15
Alignment explanation
Indices: 1218278--1218395 Score: 69
Period size: 15 Copynumber: 7.5 Consensus size: 15
1218268 AAAAGATTAG
1218278 ATAAAAATAATAATAA
1 ATAAAAA-AATAATAA
*
1218294 ATAAATAGTAATAAT-A
1 ATAAA-A-AAATAATAA
*
1218310 ATAATAATAATAA-AA
1 ATAA-AAAAATAATAA
* **
1218325 TTAACTGAAATAATAA
1 ATAA-AAAAATAATAA
* **
1218341 ATAAAAAGATAGGAA
1 ATAAAAAAATAATAA
1218356 AGTAAAAAAAATGAATAA
1 A-T-AAAAAAAT-AATAA
*
1218374 ATAAAAAAATATTAA
1 ATAAAAAAATAATAA
1218389 ATAAAAA
1 ATAAAAA
1218396 CGAAAACAAA
Statistics
Matches: 78, Mismatches: 16, Indels: 17
0.70 0.14 0.15
Matches are distributed among these distances:
15 33 0.42
16 25 0.32
17 16 0.21
18 4 0.05
ACGTcount: A:0.69, C:0.01, G:0.06, T:0.24
Consensus pattern (15 bp):
ATAAAAAAATAATAA
Found at i:1218492 original size:33 final size:31
Alignment explanation
Indices: 1218444--1218527 Score: 87
Period size: 33 Copynumber: 2.6 Consensus size: 31
1218434 AATAAGATAT
* * * *
1218444 AAAAAATAAATAAATAATAATAATGACGATGAA
1 AAAAAATTAA-AAATAAAAACAAT-ACGAAGAA
* *
1218477 AAAAATGTTAAAAATAAAAACAATATGAAGAA
1 AAAAA-ATTAAAAATAAAAACAATACGAAGAA
1218509 AAAAAATTAAAAATAAAAA
1 AAAAAATTAAAAATAAAAA
1218528 GCTTAACGGA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 13 0.30
32 11 0.26
33 16 0.37
34 3 0.07
ACGTcount: A:0.71, C:0.02, G:0.07, T:0.19
Consensus pattern (31 bp):
AAAAAATTAAAAATAAAAACAATACGAAGAA
Found at i:1218658 original size:20 final size:22
Alignment explanation
Indices: 1218629--1218674 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
1218619 ACTAAATAAC
1218629 AAAACAAGAACTTAAAAGG-CT
1 AAAACAAGAACTTAAAAGGACT
* *
1218650 AAAAC-AGAATTTTAAAGGACT
1 AAAACAAGAACTTAAAAGGACT
1218671 AAAA
1 AAAA
1218675 TAACAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.59, C:0.11, G:0.13, T:0.17
Consensus pattern (22 bp):
AAAACAAGAACTTAAAAGGACT
Found at i:1227294 original size:20 final size:20
Alignment explanation
Indices: 1227271--1227313 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1227261 AATCCACCAC
*
1227271 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
1227291 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
1227311 ATG
1 ATG
1227314 GGCTCTTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:1232261 original size:20 final size:20
Alignment explanation
Indices: 1232238--1232279 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1232228 AATCCACCAC
*
1232238 ATGCAACTATATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* *
1232258 ATGCATCTAAATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
1232278 AT
1 AT
1232280 AGGTTCTTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.31
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:1240445 original size:7 final size:7
Alignment explanation
Indices: 1240435--1240468 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
1240425 GAAAATAATT
1240435 AAAAATA
1 AAAAATA
1240442 AAAAATA
1 AAAAATA
1240449 AAAAATA
1 AAAAATA
1240456 AAAAATA
1 AAAAATA
1240463 AAAAAT
1 AAAAAT
1240469 TAAACCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:1240461 original size:21 final size:22
Alignment explanation
Indices: 1240426--1240468 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1240416 ATGAATTTTG
*
1240426 AAAATAATTAAAAATAAAAAAT
1 AAAATAATAAAAAATAAAAAAT
1240448 AAAA-AATAAAAAATAAAAAAT
1 AAAATAATAAAAAATAAAAAAT
1240469 TAAACCTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (22 bp):
AAAATAATAAAAAATAAAAAAT
Found at i:1240862 original size:17 final size:17
Alignment explanation
Indices: 1240842--1240920 Score: 56
Period size: 16 Copynumber: 4.6 Consensus size: 17
1240832 TTTAGATTAA
1240842 AATTATAAAATATAAAT
1 AATTATAAAATATAAAT
* *
1240859 AATTATTAAGATACTCAAT
1 AATTA-TAAAATA-TAAAT
*
1240878 ACATTA-AAAATAAAAAT
1 A-ATTATAAAATATAAAT
*
1240895 -ATTACAAAAT-TAAAT
1 AATTATAAAATATAAAT
* *
1240910 TATTAAAAAAT
1 AATTATAAAAT
1240921 TAATTTAAGG
Statistics
Matches: 50, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
15 8 0.16
16 14 0.28
17 8 0.16
18 11 0.22
19 5 0.10
20 4 0.08
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (17 bp):
AATTATAAAATATAAAT
Found at i:1241283 original size:16 final size:15
Alignment explanation
Indices: 1241250--1241288 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1241240 TACTCAATAC
1241250 ATTAAAAATAAAAAT
1 ATTAAAAATAAAAAT
* *
1241265 ATTACAAAATGAAATT
1 ATTA-AAAATAAAAAT
1241281 ATTAAAAA
1 ATTAAAAA
1241289 ATTAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.28
Consensus pattern (15 bp):
ATTAAAAATAAAAAT
Found at i:1241306 original size:370 final size:371
Alignment explanation
Indices: 1240618--1241361 Score: 1454
Period size: 370 Copynumber: 2.0 Consensus size: 371
1240608 AAACCGTTAA
1240618 GTTTGATCATTAACCCATTAAAATGAGGAATCAAACGTTGACAGTCACGACACTTACAAGATAGT
1 GTTTGATCATTAACCCATTAAAATGAGGAATCAAACGTTGACAGTCACGACACTTACAAGATAGT
1240683 TCTTAAACTTACATGGTAATCTAAAATTTTGATGTGACAGTTTACGATACTGTTGTGGTAGTACT
66 TCTTAAACTTACATGGTAATCTAAAATTTTGATGTGACAGTTTACGATACTGTTGTGGTAGTACT
1240748 CGATGGATGATGATATGATAGATTGCATTAATTGATTATTAAAAAGTTTAAGGACTTATTTAATT
131 CGATGGATGATGA-ATGATAGATTGCATTAATTGATTATTAAAAAGTTTAAGGACTTATTTAATT
1240813 TAAAAAAATTAAAAATTTATTTAGATTAAAATTATAAAATATAAATAATTATTAAGATACTCAAT
195 TAAAAAAATTAAAAATTTATTTAGATTAAAATTATAAAATATAAATAATTATTAAGATACTCAAT
*
1240878 ACATTAAAAATAAAAATATTACAAAATTAAATTATTAAAAAATTAATTTAAGGACTACATTGAGT
260 ACATTAAAAATAAAAATATTACAAAATGAAATTATTAAAAAATTAATTTAAGGACTACATTGAGT
1240943 GTAAAAATGTTTAGGGATCATATTGATTTTTTTATAAAAGTTTGAGT
325 GTAAAAATGTTTAGGGATCATATTGATTTTTTTATAAAAGTTTGAGT
1240990 GTTTGATCATTAACCCATTAAAATGAGGAATCAAACGTTGACAGTCACGACACTTACAAGATAGT
1 GTTTGATCATTAACCCATTAAAATGAGGAATCAAACGTTGACAGTCACGACACTTACAAGATAGT
1241055 TCTTAAACTTACATGGTAATCTAAAATTTTGATGTGACAGTTTACGATACTGTTGTGGTAGTACT
66 TCTTAAACTTACATGGTAATCTAAAATTTTGATGTGACAGTTTACGATACTGTTGTGGTAGTACT
1241120 CGATGGATGATG-ATGATAGATTGCATTAATTGATTATTAAAAAGTTTAAGGACTTATTTAATTT
131 CGATGGATGATGAATGATAGATTGCATTAATTGATTATTAAAAAGTTTAAGGACTTATTTAATTT
1241184 AAAAAAATTAAAAATTTATTTAGATTAAAATTATAAAATATAAATAATTATTAAGATACTCAATA
196 AAAAAAATTAAAAATTTATTTAGATTAAAATTATAAAATATAAATAATTATTAAGATACTCAATA
*
1241249 CATTAAAAATAAAAATATTACAAAATGAAATTATTAAAAAATTAATTTAATGACTACATTGAGTG
261 CATTAAAAATAAAAATATTACAAAATGAAATTATTAAAAAATTAATTTAAGGACTACATTGAGTG
1241314 TAAAAATGTTTAGGGATCATATTGATTTTTTTATAAAAGTTTGAGT
326 TAAAAATGTTTAGGGATCATATTGATTTTTTTATAAAAGTTTGAGT
1241360 GT
1 GT
1241362 AACACCCCAA
Statistics
Matches: 370, Mismatches: 2, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
370 228 0.62
372 142 0.38
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (371 bp):
GTTTGATCATTAACCCATTAAAATGAGGAATCAAACGTTGACAGTCACGACACTTACAAGATAGT
TCTTAAACTTACATGGTAATCTAAAATTTTGATGTGACAGTTTACGATACTGTTGTGGTAGTACT
CGATGGATGATGAATGATAGATTGCATTAATTGATTATTAAAAAGTTTAAGGACTTATTTAATTT
AAAAAAATTAAAAATTTATTTAGATTAAAATTATAAAATATAAATAATTATTAAGATACTCAATA
CATTAAAAATAAAAATATTACAAAATGAAATTATTAAAAAATTAATTTAAGGACTACATTGAGTG
TAAAAATGTTTAGGGATCATATTGATTTTTTTATAAAAGTTTGAGT
Found at i:1242522 original size:31 final size:31
Alignment explanation
Indices: 1242402--1242523 Score: 174
Period size: 31 Copynumber: 3.9 Consensus size: 31
1242392 GAATGATCAA
* * *
1242402 TCCATAGGTCCCAAATAATC-TAGGTAATCAG
1 TCCATATGTCCCAAAGAA-CATAGGTAAACAG
*
1242433 TCCATATGTCCCAAAGAACATAGGTAAATAG
1 TCCATATGTCCCAAAGAACATAGGTAAACAG
**
1242464 TCCATATGTCCTGAAGAACATAGGTAAACAG
1 TCCATATGTCCCAAAGAACATAGGTAAACAG
1242495 TCCATATGTCCCAAAGAACATAGGTAAAC
1 TCCATATGTCCCAAAGAACATAGGTAAAC
1242524 CCTCGACTCT
Statistics
Matches: 81, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
30 1 0.01
31 80 0.99
ACGTcount: A:0.39, C:0.21, G:0.16, T:0.23
Consensus pattern (31 bp):
TCCATATGTCCCAAAGAACATAGGTAAACAG
Found at i:1244582 original size:14 final size:16
Alignment explanation
Indices: 1244560--1244592 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1244550 ATGCTTTTTG
1244560 AAAATAATT-AAAATT
1 AAAATAATTAAAAATT
1244575 AAAA-AATTAAAAATT
1 AAAATAATTAAAAATT
1244590 AAA
1 AAA
1244593 CCTTTTAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAAATAATTAAAAATT
Found at i:1244699 original size:29 final size:29
Alignment explanation
Indices: 1244645--1244701 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
1244635 TGCATGTTTT
* *
1244645 TCCAGTTTAGTGCATAACGTTTATTTCGG
1 TCCAGTTTAGTGCACAACATTTATTTCGG
*
1244674 TCCAGTTTGGTGC-CAACATTTCATTTCG
1 TCCAGTTTAGTGCACAACATTT-ATTTCG
1244702 TTACTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.40
Consensus pattern (29 bp):
TCCAGTTTAGTGCACAACATTTATTTCGG
Found at i:1245684 original size:16 final size:16
Alignment explanation
Indices: 1245663--1245699 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
1245653 AAAATGATTT
1245663 TTAAAAATAATT-AAAA
1 TTAAAAA-AATTAAAAA
1245679 TTAAAAAAATTAAAAA
1 TTAAAAAAATTAAAAA
1245695 TTAAA
1 TTAAA
1245700 CCTTTTAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAAAATTAAAAA
Found at i:1245780 original size:29 final size:29
Alignment explanation
Indices: 1245738--1245797 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1245728 ATGCTTGTTT
* *
1245738 TTCCAGTTTAGTGCATAACGTTT-ATTTCG
1 TTCCAGTTTAGTGC-CAACATTTCATTTCG
*
1245767 TTCCAGTTTGGTGCCAACATTTCATTTCG
1 TTCCAGTTTAGTGCCAACATTTCATTTCG
1245796 TT
1 TT
1245798 ACTCAAAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.18, C:0.20, G:0.17, T:0.45
Consensus pattern (29 bp):
TTCCAGTTTAGTGCCAACATTTCATTTCG
Found at i:1246893 original size:18 final size:18
Alignment explanation
Indices: 1246872--1246914 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
1246862 GTTTTTAAAA
* *
1246872 AAATAAAAGATAATAATT
1 AAATAAAAGAAAATAACT
1246890 AAATAAAAGAAAATAACT
1 AAATAAAAGAAAATAACT
1246908 AAATAAA
1 AAATAAA
1246915 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAACT
Found at i:1248834 original size:31 final size:31
Alignment explanation
Indices: 1248796--1248870 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
1248786 ATGTAATAAA
* * *
1248796 AACATCATATATTTAATCAACCAGAACATAT
1 AACATCATACATTTAACCAACAAGAACATAT
* * *
1248827 ATCATCATGCATTTAACCAAGAAGAACATAT
1 AACATCATACATTTAACCAACAAGAACATAT
*
1248858 AACATCATGCATT
1 AACATCATACATT
1248871 GTTCATTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.28
Consensus pattern (31 bp):
AACATCATACATTTAACCAACAAGAACATAT
Found at i:1249003 original size:24 final size:24
Alignment explanation
Indices: 1248976--1249025 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1248966 CAGCTCGTAT
*
1248976 AAATTGCACCGAAGTGCCGCATAG
1 AAATTGCACCGAAGTGCCACATAG
*
1249000 AAATTGCACTGAAGTGCCACATAG
1 AAATTGCACCGAAGTGCCACATAG
1249024 AA
1 AA
1249026 GTGTCCCGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (24 bp):
AAATTGCACCGAAGTGCCACATAG
Found at i:1250262 original size:2 final size:2
Alignment explanation
Indices: 1250255--1250337 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
1250245 AAGGGAAAAG
1250255 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1250297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1250338 CACGTTATAA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1251614 original size:20 final size:19
Alignment explanation
Indices: 1251589--1251632 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1251579 TTTTCTTTCC
1251589 TTTCT-GGTTTGAATCTCTCT
1 TTTCTGGGTTTG-ATC-CTCT
*
1251609 TTTCTGGGTTTGTTCCTCT
1 TTTCTGGGTTTGATCCTCT
1251628 TTTCT
1 TTTCT
1251633 TTTTTGTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 9 0.41
20 7 0.32
21 6 0.27
ACGTcount: A:0.05, C:0.20, G:0.16, T:0.59
Consensus pattern (19 bp):
TTTCTGGGTTTGATCCTCT
Found at i:1252814 original size:2 final size:2
Alignment explanation
Indices: 1252807--1252842 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1252797 ATTGAATTTA
1252807 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1252843 GAACCGAGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1257467 original size:72 final size:73
Alignment explanation
Indices: 1257391--1257530 Score: 174
Period size: 72 Copynumber: 1.9 Consensus size: 73
1257381 TTATAATTTT
* ** * * *
1257391 AAAATTTATTTTCAGAAAATATCTCTAACTGTTGATTA-TTTTTATTGAATTTAAAATTAATTAT
1 AAAATGTATTTTCAGAAAATAGATCTAACTATTAATTATTTTTTATTGAATTTAAAATTAATCAT
1257455 TTTAATTC
66 TTTAATTC
* * ** *
1257463 AAAATGTATTTTCATAAAATAGATTTATTTATTAATTATTTTTTATTTAATTTAAAATTAATCAT
1 AAAATGTATTTTCAGAAAATAGATCTAACTATTAATTATTTTTTATTGAATTTAAAATTAATCAT
1257528 TTT
66 TTT
1257531 GAAAATATTT
Statistics
Matches: 56, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
72 29 0.52
73 27 0.48
ACGTcount: A:0.39, C:0.05, G:0.04, T:0.52
Consensus pattern (73 bp):
AAAATGTATTTTCAGAAAATAGATCTAACTATTAATTATTTTTTATTGAATTTAAAATTAATCAT
TTTAATTC
Found at i:1261046 original size:55 final size:56
Alignment explanation
Indices: 1260986--1261144 Score: 146
Period size: 55 Copynumber: 2.8 Consensus size: 56
1260976 GTGTACTTTC
1260986 TCTTTCATATATCTCATATCACATAGCTCATATTATTCATTCACCTATCATATGTA
1 TCTTTCATATATCTCATATCACATAGCTCATATTATTCATTCACCTATCATATGTA
* * * * * * * *
1261042 -CTTTC-TCTTTCACTTA-CACGTAGAAT-ATTTTCATATGATTCACCTATCATATGTA
1 TCTTTCATATATCTCATATCACATAG-CTCATATT-AT-TCATTCACCTATCATATGTA
1261097 TTTTCTCTTTCATATATCTCATATCACATAGCTCATATTATTCATTCA
1 -----TCTTTCATATATCTCATATCACATAGCTCATATTATTCATTCA
1261145 AATCATATCA
Statistics
Matches: 75, Mismatches: 16, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
53 10 0.13
54 10 0.13
55 24 0.32
61 11 0.15
62 10 0.13
63 10 0.13
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (56 bp):
TCTTTCATATATCTCATATCACATAGCTCATATTATTCATTCACCTATCATATGTA
Found at i:1261912 original size:12 final size:12
Alignment explanation
Indices: 1261897--1261944 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
1261887 ATCGACTTCC
1261897 AAATTCATTTAA
1 AAATTCATTTAA
1261909 AAATTCTATTTCAA
1 AAATTC-ATTT-AA
* *
1261923 TAATTCACTTAA
1 AAATTCATTTAA
*
1261935 AAACTCATTT
1 AAATTCATTT
1261945 TTCTTAATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
12 15 0.52
13 7 0.24
14 7 0.24
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (12 bp):
AAATTCATTTAA
Found at i:1270073 original size:31 final size:29
Alignment explanation
Indices: 1270012--1270073 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
1270002 TGTTTTTCAC
*
1270012 TTTTGATCACTAATTTTAAATTAGTTATT
1 TTTTGATCACTAATTATAAATTAGTTATT
* *
1270041 TTTTGATCACTTATATTATCAATTTGTTATT
1 TTTTGATCAC-TA-ATTATAAATTAGTTATT
1270072 TT
1 TT
1270074 ATCATTAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 10 0.36
30 2 0.07
31 16 0.57
ACGTcount: A:0.27, C:0.08, G:0.06, T:0.58
Consensus pattern (29 bp):
TTTTGATCACTAATTATAAATTAGTTATT
Found at i:1272099 original size:35 final size:35
Alignment explanation
Indices: 1272028--1272139 Score: 99
Period size: 35 Copynumber: 3.2 Consensus size: 35
1272018 GTGGTAAGAA
* * * *
1272028 ATTTATTTTTA-T-GATAGTATTTTTTTAAATAGTT
1 ATTTATTTTTATTAAATAATATTTATATAAATA-TT
*
1272062 ATTATATTTTATATT-AAT-ATATTTATGTAAATATT
1 ATT-TATTTT-TATTAAATAATATTTATATAAATATT
*
1272097 ATTT-TTTTTATTAAAATAATATTTATATAATTATT
1 ATTTATTTTTATT-AAATAATATTTATATAAATATT
1272132 ATTTATTT
1 ATTTATTT
1272140 AGAATTATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
32 4 0.06
33 4 0.06
34 7 0.11
35 30 0.46
36 17 0.26
37 3 0.05
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (35 bp):
ATTTATTTTTATTAAATAATATTTATATAAATATT
Done.