Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008550.1 Hibiscus syriacus cultivar Beakdansim tig00111445_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: 1154708
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
File 6 of 6
Found at i:1022348 original size:15 final size:15
Alignment explanation
Indices: 1022328--1022367 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
1022318 AATAAATTCA
*
1022328 TCAAAATTTAGAGGT
1 TCAAAATTCAGAGGT
*
1022343 TCAAAATTCAGATGT
1 TCAAAATTCAGAGGT
1022358 TCAAAATTCA
1 TCAAAATTCA
1022368 TACCTGATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (15 bp):
TCAAAATTCAGAGGT
Found at i:1024809 original size:15 final size:14
Alignment explanation
Indices: 1024789--1024818 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
1024779 CTTCATTTTC
1024789 TATTATTATTTATAT
1 TATTATTATTT-TAT
1024804 TATTATTATTTTAT
1 TATTATTATTTTAT
1024818 T
1 T
1024819 TTTTTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (14 bp):
TATTATTATTTTAT
Found at i:1026409 original size:22 final size:22
Alignment explanation
Indices: 1026375--1026418 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1026365 GGTAATTTAA
1026375 AATTAAATATTATAAAAATTAT
1 AATTAAATATTATAAAAATTAT
* * **
1026397 AATTTAATTTTATTTAAATTAT
1 AATTAAATATTATAAAAATTAT
1026419 TATATTGTTA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATTAAATATTATAAAAATTAT
Found at i:1037617 original size:20 final size:19
Alignment explanation
Indices: 1037592--1037668 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
1037582 ATTATGCTTG
*
1037592 AAGAAAAAAGAAGAACAAAA
1 AAGAAAAAA-AAGAAAAAAA
**
1037612 AAGAAAAAAAATGAGGAAAA
1 AAGAAAAAAAA-GAAAAAAA
1037632 AAGAAAGAAAAAGAAAAAAA
1 AAGAAA-AAAAAGAAAAAAA
*
1037652 AAG-AAAAGAAGAAAAAA
1 AAGAAAAAAAAGAAAAAA
1037669 GAGGGGGTCA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
18 11 0.22
19 4 0.08
20 30 0.60
21 5 0.10
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (19 bp):
AAGAAAAAAAAGAAAAAAA
Found at i:1037670 original size:10 final size:9
Alignment explanation
Indices: 1037592--1037668 Score: 75
Period size: 10 Copynumber: 8.0 Consensus size: 9
1037582 ATTATGCTTG
1037592 AAGAAAAAA
1 AAGAAAAAA
1037601 GAAGAACAAAA
1 -AAGAA-AAAA
1037612 AAGAAAAAA
1 AAGAAAAAA
*
1037621 AATGAGGAAAA
1 AA-GA-AAAAA
1037632 AAGAAAGAAA
1 AAGAAA-AAA
1037642 AAGAAAAAA
1 AAGAAAAAA
*
1037651 AA-AGAAAAG
1 AAGA-AAAAA
1037660 AAGAAAAAA
1 AAGAAAAAA
1037669 GAGGGGGTCA
Statistics
Matches: 57, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
8 1 0.02
9 22 0.39
10 24 0.42
11 10 0.18
ACGTcount: A:0.81, C:0.01, G:0.17, T:0.01
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:1038065 original size:19 final size:17
Alignment explanation
Indices: 1038023--1038071 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
1038013 TATTTTCTCT
1038023 AAATTCAATTTA-TTTG
1 AAATTCAATTTATTTTG
*
1038039 AGATTCAATTTATTTTCG
1 AAATTCAATTTATTTT-G
*
1038057 AAAATTCAACTTATT
1 -AAATTCAATTTATT
1038072 CTTTTATTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 3 0.11
18 1 0.04
19 12 0.44
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.47
Consensus pattern (17 bp):
AAATTCAATTTATTTTG
Found at i:1038565 original size:114 final size:114
Alignment explanation
Indices: 1038365--1038701 Score: 566
Period size: 114 Copynumber: 3.0 Consensus size: 114
1038355 TACCCCGTTA
1038365 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
*
1038430 TTTGATATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAATTTGC
66 TTTGGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAATTTGC
1038479 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* *
1038544 TTTGGTATGAACCCCAAAATCAATCATTGGATTTGAAAGATGAATTTGT
66 TTTGGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAATTTGC
* * * *
1038593 TTATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTTTTCTTTGAGTCATCTGATCTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
* * * * *
1038658 TTCGGTAAGAACCACAAAACCAATCATTGGAATTAAAAGATGAA
66 TTTGGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAA
1038702 CTACATGATC
Statistics
Matches: 210, Mismatches: 13, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 210 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.31
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGA
TTTGGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAATTTGC
Found at i:1039851 original size:116 final size:110
Alignment explanation
Indices: 1039654--1040090 Score: 432
Period size: 116 Copynumber: 3.8 Consensus size: 110
1039644 GATCAGCATT
* *
1039654 AACATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
1 AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAA-GAAGAAGAA-TTCATAAT
* * * *
1039719 GAGAAGAATTTGTTCAACCTTTTGTTTGAATTCATCATTTGATGGATC
64 GAGAAGAATTTGTTCAACCTTTTG-CTAAATCCATCACTTGATGGATC
*
1039767 AACATTGCCAGGTAGAGTTCATAATGAGAAGAACTCGTCATCTGAAGAAGAAAGAAGAAATTCAT
1 AACATTTCCAGGTAGAGTTCATAATGAGAAGAA--C-TCATCTGAAGAAG-AAGAAG-AATTCAT
1039832 AATGAGAAGAATTTGTTCAACCTTTTGCTAAATCCATCACTTGATGGATC
61 AATGAGAAGAATTTGTTCAACCTTTTGCTAAATCCATCACTTGATGGATC
* * *
1039882 AACTTTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAG--TTCACAATG
1 AACATTTCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAATTCATAATG
** * * ** *
1039944 AGAAGAGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAAGAGATAGATTAGC
65 AGAAGAATTTGTTCAACCTTTTGC-TAAATCCATCAC-----TTGATGGA-T--C
* *
1039999 ATCAATCTCTCCAGAG-AAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCA
1 AAC-AT-T-TCCAG-GTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAG-AAGAAGAA-TTCA
** *
1040063 TAATGAGAAGAGCTTATTCAACCTTTTG
60 TAATGAGAAGAATTTGTTCAACCTTTTG
1040091 AATGACTCTA
Statistics
Matches: 280, Mismatches: 22, Indels: 33
0.84 0.07 0.10
Matches are distributed among these distances:
108 30 0.11
109 10 0.04
111 6 0.02
112 13 0.05
113 31 0.11
114 5 0.02
115 50 0.18
116 51 0.18
117 5 0.02
118 1 0.00
119 1 0.00
120 41 0.15
121 6 0.02
124 30 0.11
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (110 bp):
AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAATTCATAATGA
GAAGAATTTGTTCAACCTTTTGCTAAATCCATCACTTGATGGATC
Found at i:1040105 original size:124 final size:122
Alignment explanation
Indices: 1039888--1040178 Score: 405
Period size: 124 Copynumber: 2.4 Consensus size: 122
1039878 GATCAACTTT
1039888 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCT---GAAG-AAGAAGAAGTTCACAATGAGAAG
1 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAG
* * * * * *
1039949 AGCTTGTTCAACCTTTTGCATAATTCTATCACAGAAAGAGATAGATTAGCATCAATCTC
66 AGCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATAAACATC-ATC-C
*
1040008 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATGAGAAG
1 TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAG
* * *
1040073 AGCTTATTCAACCTTTTGAATGACTCTATCACAGAAGGAAATAGGTAAACATCATCC
66 AGCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATAAACATCATCC
* *
1040130 -CCAGCGGAAAGTTCATAATGAGAAGAACTCATCTGAAGAA-AGAGAAGAA
1 TCCAG-AGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAA
1040179 TTTATTCAAC
Statistics
Matches: 154, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
120 34 0.22
121 12 0.08
122 35 0.23
123 7 0.05
124 66 0.43
ACGTcount: A:0.42, C:0.16, G:0.20, T:0.22
Consensus pattern (122 bp):
TCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCACAATGAGAAG
AGCTTATTCAACCTTTTGAATAACTCTATCACAGAAAGAAATAGATAAACATCATCC
Found at i:1040325 original size:3 final size:3
Alignment explanation
Indices: 1040319--1040368 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
1040309 TCTCCATTTT
* **
1040319 TTA TTA TTA TT- TATA TTA TTA TTA TT- TTA TTT TTA TTA AAA TTA
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1040363 TTA TTA
1 TTA TTA
1040369 CAAACGGGCC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
2 3 0.08
3 34 0.89
4 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:1040339 original size:15 final size:14
Alignment explanation
Indices: 1040314--1040356 Score: 61
Period size: 15 Copynumber: 3.1 Consensus size: 14
1040304 TTTTTTCTCC
1040314 ATTTT-TTATTATT
1 ATTTTATTATTATT
1040327 ATTTATATTATTATT
1 ATTT-TATTATTATT
*
1040342 ATTTTATTTTTATT
1 ATTTTATTATTATT
1040356 A
1 A
1040357 AAATTATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 4 0.15
14 11 0.41
15 12 0.44
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTTTATTATTATT
Found at i:1040347 original size:26 final size:26
Alignment explanation
Indices: 1040317--1040368 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
1040307 TTTCTCCATT
* *
1040317 TTTTATTATTATTTATATTATTATTA
1 TTTTATTATTATTAAAATTATTATTA
*
1040343 TTTTATTTTTATTAAAATTATTATTA
1 TTTTATTATTATTAAAATTATTATTA
1040369 CAAACGGGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTATTATTATTAAAATTATTATTA
Found at i:1041799 original size:28 final size:27
Alignment explanation
Indices: 1041725--1041800 Score: 64
Period size: 29 Copynumber: 2.7 Consensus size: 27
1041715 GTTCTAATTG
** *
1041725 TATTTTTATTATTGTT-TATTTATGTTT
1 TATTTTTATTATT-TTATATTTAAATAT
* *
1041752 TAATTTTACTTGTTTATATATTTAAATAT
1 TATTTTTA-TTATTT-TATATTTAAATAT
1041781 TATTTTTATTATTATTATAT
1 TATTTTTATTATT-TTATAT
1041801 AGTCATATAA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
27 8 0.21
28 14 0.37
29 16 0.42
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (27 bp):
TATTTTTATTATTTTATATTTAAATAT
Found at i:1048328 original size:2 final size:2
Alignment explanation
Indices: 1048321--1048413 Score: 186
Period size: 2 Copynumber: 46.5 Consensus size: 2
1048311 TAACTATAAT
1048321 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
1048363 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
1048405 TA TA TA TA T
1 TA TA TA TA T
1048414 GTGTGTGTGT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 91 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1059489 original size:33 final size:33
Alignment explanation
Indices: 1059444--1059519 Score: 134
Period size: 33 Copynumber: 2.3 Consensus size: 33
1059434 CGACCAACAC
1059444 ACACCAAACTCAAGACAATATATGTGACGGGAGA
1 ACACC-AACTCAAGACAATATATGTGACGGGAGA
*
1059478 ACACCAACTCAAGACAATATATGTGACTGGAGA
1 ACACCAACTCAAGACAATATATGTGACGGGAGA
1059511 ACACCAACT
1 ACACCAACT
1059520 AATTTACTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
33 36 0.88
34 5 0.12
ACGTcount: A:0.43, C:0.24, G:0.17, T:0.16
Consensus pattern (33 bp):
ACACCAACTCAAGACAATATATGTGACGGGAGA
Found at i:1062872 original size:47 final size:47
Alignment explanation
Indices: 1062816--1062910 Score: 181
Period size: 47 Copynumber: 2.0 Consensus size: 47
1062806 ATCGCCATGA
*
1062816 ATGAAGAAATGCAATCCCTTCAAAAGAATCAGCCGTGGAAACTAGCT
1 ATGAAGAAATGCAATCCCTTCAAAAGAATCAGACGTGGAAACTAGCT
1062863 ATGAAGAAATGCAATCCCTTCAAAAGAATCAGACGTGGAAACTAGCT
1 ATGAAGAAATGCAATCCCTTCAAAAGAATCAGACGTGGAAACTAGCT
1062910 A
1 A
1062911 GTCTTCCGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.42, C:0.20, G:0.19, T:0.19
Consensus pattern (47 bp):
ATGAAGAAATGCAATCCCTTCAAAAGAATCAGACGTGGAAACTAGCT
Found at i:1063131 original size:60 final size:61
Alignment explanation
Indices: 1063038--1063157 Score: 233
Period size: 60 Copynumber: 2.0 Consensus size: 61
1063028 AAATGGAGGG
1063038 AATTGATTATAATGAAGTATTTTCTCCAGTTGTAAAAC-TTCCTCCATCAGAATTTTGTTT
1 AATTGATTATAATGAAGTATTTTCTCCAGTTGTAAAACATTCCTCCATCAGAATTTTGTTT
1063098 AATTGATTATAATGAAGTATTTTCTCCAGTTGTAAAACATTCCTCCATCAGAATTTTGTT
1 AATTGATTATAATGAAGTATTTTCTCCAGTTGTAAAACATTCCTCCATCAGAATTTTGTT
1063158 GGCTTTGGTA
Statistics
Matches: 59, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 38 0.64
61 21 0.36
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (61 bp):
AATTGATTATAATGAAGTATTTTCTCCAGTTGTAAAACATTCCTCCATCAGAATTTTGTTT
Found at i:1071725 original size:31 final size:33
Alignment explanation
Indices: 1071689--1071755 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
1071679 GACACAAAAC
1071689 AATATT-AAAAATCCACTAAC-AAGATAAAAGA
1 AATATTAAAAAATCCACTAACAAAGATAAAAGA
1071720 AATATTAAAAAATCCACTAACTAAAGATAAAAGA
1 AATATTAAAAAATCCACTAAC-AAAGATAAAAGA
1071754 AA
1 AA
1071756 CAATTAGCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
31 6 0.18
32 14 0.42
34 13 0.39
ACGTcount: A:0.63, C:0.12, G:0.06, T:0.19
Consensus pattern (33 bp):
AATATTAAAAAATCCACTAACAAAGATAAAAGA
Found at i:1074335 original size:33 final size:33
Alignment explanation
Indices: 1074288--1074353 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1074278 TTTATACTAC
* *
1074288 ACACTCAAATGGTCATCTTGATGATCGCTCAAA
1 ACACTCAAACGGTCATCTTAATGATCGCTCAAA
1074321 ACACTCAAACGGTCATCTTAATGATCGCTCAAA
1 ACACTCAAACGGTCATCTTAATGATCGCTCAAA
1074354 CTACTGTGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.26
Consensus pattern (33 bp):
ACACTCAAACGGTCATCTTAATGATCGCTCAAA
Found at i:1082836 original size:76 final size:76
Alignment explanation
Indices: 1082673--1082825 Score: 236
Period size: 76 Copynumber: 2.0 Consensus size: 76
1082663 GGAAAACGAG
* * *
1082673 AGAAAAGGAAGAGATTTTGGATGCTGAGCGGGGAAAAAGATAGACCGAAAATAAAGGATGGAGGG
1 AGAAAAGGGAGAGATTTTGGATGCTGAGCGGGGAAAAAGAGAGACCGAAAATAAAGGAGGGAGGG
1082738 TTTGGCCAGGA
66 TTTGGCCAGGA
* *
1082749 AGAAAAGGGAGAGCTTTTGGATGCTGAGC-GGGAAAGAAGAGAGATCGAAAATAAAGGAGGGAGG
1 AGAAAAGGGAGAGATTTTGGATGCTGAGCGGGGAAA-AAGAGAGACCGAAAATAAAGGAGGGAGG
*
1082813 GTTTGGCCGGGA
65 GTTTGGCCAGGA
1082825 A
1 A
1082826 TAGGCGGGAG
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
75 6 0.09
76 64 0.91
ACGTcount: A:0.38, C:0.08, G:0.39, T:0.15
Consensus pattern (76 bp):
AGAAAAGGGAGAGATTTTGGATGCTGAGCGGGGAAAAAGAGAGACCGAAAATAAAGGAGGGAGGG
TTTGGCCAGGA
Found at i:1082929 original size:15 final size:16
Alignment explanation
Indices: 1082909--1082953 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 16
1082899 CTATTTAAAA
1082909 TTAATATTAATATAT-
1 TTAATATTAATATATC
1082924 TTAATATTAATACTATC
1 TTAATATTAATA-TATC
1082941 TT-ATATTAATATA
1 TTAATATTAATATA
1082954 ATATAATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 14 0.50
16 12 0.43
17 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATATTAATATATC
Found at i:1083024 original size:31 final size:31
Alignment explanation
Indices: 1082972--1083031 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
1082962 TGTAATTAAT
*
1082972 ATTAATACTAATATAAAATATAGTCTATAAA
1 ATTAATACTAATATAAAATATAGTATATAAA
* *
1083003 ATTAATATTAATA-AATTATATAGTATATA
1 ATTAATACTAATATAA-AATATAGTATATA
1083032 TTATAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.40
Consensus pattern (31 bp):
ATTAATACTAATATAAAATATAGTATATAAA
Found at i:1083032 original size:22 final size:22
Alignment explanation
Indices: 1083007--1083065 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
1082997 TATAAAATTA
*
1083007 ATATTAATAAATTATATAGTAT
1 ATATTAATAAATTATATACTAT
* *
1083029 ATATT-ATAAACTATCTACTAT
1 ATATTAATAAATTATATACTAT
*
1083050 AT-TAATATAAATTATA
1 ATATTA-ATAAATTATA
1083066 GTTAAGATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
20 1 0.03
21 15 0.52
22 13 0.45
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (22 bp):
ATATTAATAAATTATATACTAT
Found at i:1083050 original size:21 final size:21
Alignment explanation
Indices: 1083007--1083065 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
1082997 TATAAAATTA
* *
1083007 ATATTAATAAATTATATAGTAT
1 ATATT-ATAAACTATATACTAT
*
1083029 ATATTATAAACTATCTACTAT
1 ATATTATAAACTATATACTAT
* *
1083050 ATTAATATAAATTATA
1 A-TATTATAAACTATA
1083066 GTTAAGATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 14 0.47
22 16 0.53
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (21 bp):
ATATTATAAACTATATACTAT
Found at i:1083263 original size:63 final size:63
Alignment explanation
Indices: 1083136--1083263 Score: 154
Period size: 61 Copynumber: 2.1 Consensus size: 63
1083126 AACTCTAGGT
* * *
1083136 TATATATATAGTTTATATAACGTATAAATAAATTGTATATATACATATACTATAGGTTATATA
1 TATATATATAGTTTATATAACGTATAAATAAATTGCATACATACATATACTATAAGTTATATA
* ** * *
1083199 TATATATATAGTTTGTATATAC-TATGCAT-AATT-CATACATACATGTACTATAAGTTACATA
1 TATATATATAGTTTATATA-ACGTATAAATAAATTGCATACATACATATACTATAAGTTATATA
1083260 TATA
1 TATA
1083264 GTTTACATGT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
61 27 0.48
62 4 0.07
63 23 0.41
64 2 0.04
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (63 bp):
TATATATATAGTTTATATAACGTATAAATAAATTGCATACATACATATACTATAAGTTATATA
Found at i:1083485 original size:80 final size:82
Alignment explanation
Indices: 1083401--1083552 Score: 204
Period size: 82 Copynumber: 1.9 Consensus size: 82
1083391 TATATATATA
* *
1083401 TATATATTCTATAGA-TTACTTATATTAG-TTATACATAT-ATATATATATATACTATATTAATA
1 TATATATTCTATAGAGTT--TTATAATAGTTTATACATATAATACATATATATACTATATTAATA
1083463 T-AATTATAATTTACAAAC
64 TAAATTATAATTTACAAAC
* * *
1083481 TATATATTTTATATAGTTTTATAATAGTTTATATATATACATACATATATATACTATATTAATAT
1 TATATATTCTATAGAGTTTTATAATAGTTTATACATATA-ATACATATATATACTATATTAATAT
1083546 AAATTAT
65 AAATTAT
1083553 TTTTATAACT
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
79 8 0.13
80 22 0.35
81 2 0.03
82 24 0.39
83 6 0.10
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (82 bp):
TATATATTCTATAGAGTTTTATAATAGTTTATACATATAATACATATATATACTATATTAATATA
AATTATAATTTACAAAC
Found at i:1083641 original size:20 final size:20
Alignment explanation
Indices: 1083590--1083679 Score: 78
Period size: 20 Copynumber: 4.5 Consensus size: 20
1083580 TATATAAATT
1083590 GTATA-AAATATAGTATATA
1 GTATATAAATATAGTATATA
* *
1083609 -AATATAAACTATAGTATGTA
1 GTATATAAA-TATAGTATATA
*
1083629 GTATATAAATATA-AACTATA
1 GTATATAAATATAGTA-TATA
* * *
1083649 ATTTATATATATAGTATATA
1 GTATATAAATATAGTATATA
*
1083669 CTATATAAATA
1 GTATATAAATA
1083680 GTTTATATAG
Statistics
Matches: 54, Mismatches: 12, Indels: 9
0.72 0.16 0.12
Matches are distributed among these distances:
18 3 0.06
19 4 0.07
20 39 0.72
21 8 0.15
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (20 bp):
GTATATAAATATAGTATATA
Found at i:1083667 original size:27 final size:27
Alignment explanation
Indices: 1083591--1083686 Score: 99
Period size: 27 Copynumber: 3.7 Consensus size: 27
1083581 ATATAAATTG
*
1083591 TATAAAATATAGTATATAAATATAAAC
1 TATAATATATAGTATATAAATATAAAC
* *
1083618 TATAGTATGTAGTATATAAATATAAAC
1 TATAATATATAGTATATAAATATAAAC
* * *
1083645 TATAATTTATA-TATAT-AGTATATAC
1 TATAATATATAGTATATAAATATAAAC
* *
1083670 TAT-ATAAATAGTTTATA
1 TATAATATATAGTATATA
1083687 TAGTTTACTA
Statistics
Matches: 56, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
24 5 0.09
25 14 0.25
26 5 0.09
27 32 0.57
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (27 bp):
TATAATATATAGTATATAAATATAAAC
Found at i:1083673 original size:18 final size:18
Alignment explanation
Indices: 1083652--1083686 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1083642 AACTATAATT
*
1083652 TATATATATAGTATATAC
1 TATATAAATAGTATATAC
*
1083670 TATATAAATAGTTTATA
1 TATATAAATAGTATATA
1083687 TAGTTTACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
TATATAAATAGTATATAC
Found at i:1083960 original size:22 final size:24
Alignment explanation
Indices: 1083926--1083984 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
1083916 ATAATATATA
*
1083926 TATATATATATAAACTATACAGTT
1 TATATATATATAAACTATACAATT
*
1083950 TATAT-TA-ATAAACTATATAATT
1 TATATATATATAAACTATACAATT
*
1083972 TATACAATATATA
1 TATA-TATATATA
1083985 TTATTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 17 0.59
23 2 0.07
24 7 0.24
25 3 0.10
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (24 bp):
TATATATATATAAACTATACAATT
Found at i:1084123 original size:2 final size:2
Alignment explanation
Indices: 1084116--1084295 Score: 145
Period size: 2 Copynumber: 88.0 Consensus size: 2
1084106 TTATACATGT
* * * *
1084116 TA TA TA TA GTT TA TA CA TA -A TA TA TA TA GTT TA TA TA GTT TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA -TA TA
* * *
1084158 TA TA TA GTA TA TA -A TA -A TA TA AA TA TA AA CTA TA TA GTT TA
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * *
1084199 TA TA TA TA -A TA CA TA TA CTT TA TA TA TA AA CTA TA TA GTT TA
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA TA TA -TA TA
1084241 TA T- 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
1084282 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
1084296 GTTGTTTCAG
Statistics
Matches: 142, Mismatches: 22, Indels: 28
0.74 0.11 0.15
Matches are distributed among these distances:
1 5 0.04
2 127 0.89
3 10 0.07
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:1084130 original size:9 final size:9
Alignment explanation
Indices: 1084100--1084161 Score: 61
Period size: 9 Copynumber: 6.4 Consensus size: 9
1084090 TATTTAGTAT
1084100 TATAGTTTA
1 TATAGTTTA
*
1084109 TACATGTTATA
1 TATA-GTT-TA
1084120 TATAGTTTA
1 TATAGTTTA
* *
1084129 TACATAATATA
1 T--ATAGTTTA
1084140 TATAGTTTA
1 TATAGTTTA
1084149 TATAGTTTA
1 TATAGTTTA
1084158 TATA
1 TATA
1084162 TAGTATATAA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
9 25 0.58
10 6 0.14
11 12 0.28
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.50
Consensus pattern (9 bp):
TATAGTTTA
Found at i:1084909 original size:210 final size:214
Alignment explanation
Indices: 1084392--1085104 Score: 1091
Period size: 216 Copynumber: 3.3 Consensus size: 214
1084382 ATGATCTCTT
* *
1084392 TGTGTTGTTTAATTTATTTAAATTTTAATTTATAATTTCATATTTTTTCAATTTAGTCCTTAAAA
1 TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAA
* * * * ** *
1084457 TTATATTTACATCTGAAATTGACCAATACTAATTACTTATTTTTATTTTTTAATTGGCTTATAAA
66 TTATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAAC
*
1084522 TTTTTAAATGGGTATAATTTATTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTT
131 TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTT
* *
1084587 TGATTTGATCCCTCATCAATG
196 CGATTTGATCCCTCAT--ATA
* * *
1084608 TGTGTTGTTTAATTTATTTATATTTTAATTTTTAATTTCATATTTGTTCAATTTAGTCATTAAAA
1 TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAA
1084673 TTATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAAC
66 TTATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAAC
*
1084738 TTTTTTAAATGGGTATAATTTAGTACTTTTTCGTATTAATTTAAACCTCACAATTTAAAATTATT
131 -TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATT
1084803 TCGATTTGAT-CC-C-T-T-
195 TCGATTTGATCCCTCATATA
* *
1084818 TGTGTTGTTTAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTTAATTTAGTCC-TATAA
1 TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTA-AA
1084882 ATTATATTTGCATCTGAAATTGACCCATACTTATTACTT-TTTATA-TTTTTAATTGGCCCATAA
65 ATTATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAA
* *
1084945 CTTTTTAAATGGGTAAAATTTAGTACTTTTTTGTATTAATTTCAACCTCACAATTTAAAATTATT
130 CTTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATT
*
1085010 TTGATTTGATCCCTCATCAATA
195 TCGATTTGATCCCTCAT--ATA
* * *
1085032 TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAATTCTTAAAT
1 TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAA
*
1085097 TTGTATTT
66 TTATATTT
1085105 TTCATAAAAT
Statistics
Matches: 458, Mismatches: 29, Indels: 22
0.90 0.06 0.04
Matches are distributed among these distances:
207 70 0.15
208 21 0.05
209 9 0.02
210 96 0.21
211 1 0.00
213 1 0.00
214 65 0.14
215 3 0.01
216 121 0.26
217 71 0.16
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (214 bp):
TGTGTTGTTTAATTTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTAAAA
TTATATTTGCATCTGAAATTGACCCATACTTATTACTTATTTATATTTTTTAATTGGCCCATAAC
TTTTTAAATGGGTATAATTTAGTACTTTTTTGTATTAATTTAAACCTCACAATTTAAAATTATTT
CGATTTGATCCCTCATATA
Found at i:1085483 original size:21 final size:21
Alignment explanation
Indices: 1085457--1085551 Score: 138
Period size: 21 Copynumber: 4.5 Consensus size: 21
1085447 CTAAAAATGT
*
1085457 CCCGACCTGATTTGACATGAA
1 CCCGACCTGATTTGACCTGAA
* *
1085478 CCCGACTTGATTTGACCTAAA
1 CCCGACCTGATTTGACCTGAA
1085499 CCCGACCTGATTTGACCTGAA
1 CCCGACCTGATTTGACCTGAA
*
1085520 TCCGACCTGATTTGACCT-AGA
1 CCCGACCTGATTTGACCTGA-A
1085541 CCCGACCTGAT
1 CCCGACCTGAT
1085552 CTGAGTTGAA
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 1 0.02
21 65 0.98
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (21 bp):
CCCGACCTGATTTGACCTGAA
Found at i:1085525 original size:42 final size:42
Alignment explanation
Indices: 1085457--1085551 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
1085447 CTAAAAATGT
*
1085457 CCCGACCTGATTTGACATGAACCCGACTTGATTTGACCTAAA
1 CCCGACCTGATTTGACATGAACCCGACCTGATTTGACCTAAA
* * *
1085499 CCCGACCTGATTTGACCTGAATCCGACCTGATTTGACCTAGA
1 CCCGACCTGATTTGACATGAACCCGACCTGATTTGACCTAAA
1085541 CCCGACCTGAT
1 CCCGACCTGAT
1085552 CTGAGTTGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.25, C:0.32, G:0.18, T:0.25
Consensus pattern (42 bp):
CCCGACCTGATTTGACATGAACCCGACCTGATTTGACCTAAA
Found at i:1088457 original size:4 final size:4
Alignment explanation
Indices: 1088448--1089832 Score: 2200
Period size: 4 Copynumber: 359.2 Consensus size: 4
1088438 TCACATTGTG
1088448 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1088496 ACAT ACAT ACAT ACAT ACAT -C-T ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1088542 AC-T ACA- ACAT --AT ACAT ACA- ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1088585 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1088633 -CAT ACAT ACAT ACAT ACAT ACAT ACAG ACAT AC-T ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1088679 ACAT -CAT ACAT ACAT ACAT -CTAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT ACAT ACAT ACAT
1088726 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1088772 ACAT ACAT ACAT ACAT ACCAT ACAT ACAT ACAT ACAT ACAT ACAT ACCT
1 ACAT ACAT ACAT ACAT A-CAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1088821 ACAT ACAT ACAT ACAT ACAT ACAG AC-- ACAT ACAT ACAT ACAT AC-T
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1088866 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT ACCT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1088913 ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT AC-- ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1088958 ACAT ACAT ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1089004 ACAT ACAT ACAT ACAT AC-T A-AT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
1089050 ACAG ACAT AAAT ACAT ACAT --AT ACAT ACAT --AT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1089094 ACAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT AC-T
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1089140 ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1089187 ACAT -CAT ACAT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT AACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -ACAT
*
1089234 ACAT ACAT ACAT ACAT ACCT ACAT ACAT AC-T ACAT ACAT -CAT AC--
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
1089278 ACAT ACAT -CCT ACAT ACAT ACAT ACAT -CAT ACAT ACAT ACAC ATCAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A-CAT
1089325 ACAAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT AC-T
1 AC-AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1089372 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAC ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1089418 ACAT A-AT ACAT ACAT ACAT --AT ACAT ACCT ACAT ACAT AC-T ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1089462 ACAT ACAT ACAT ACCT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1089510 --AT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1089556 ACAT ACAT ACAT ACAT ACAT ACAT ACA- ACAT AC-T ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1089602 --AT ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACCT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1089647 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -CAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1089694 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT -CAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1089741 ACAT ACAT ACAT AC-T ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
1089788 ACCT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1089833 TGTATGTGTG
Statistics
Matches: 1292, Mismatches: 27, Indels: 124
0.90 0.02 0.09
Matches are distributed among these distances:
2 25 0.02
3 90 0.07
4 1161 0.90
5 16 0.01
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:1090791 original size:162 final size:161
Alignment explanation
Indices: 1090524--1091027 Score: 611
Period size: 162 Copynumber: 3.0 Consensus size: 161
1090514 ACGAAAAGAT
*
1090524 AAAACCGGTAAAGCGCTACTGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
1 AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* * * * *
1090589 TGTGAATTTAAAAGAGAAACAATTTTAGCGACC-GTAAAGTGTCGATACTTTATAAAAATATATC
66 TGTGAATTTAAAAGA-AAACAGTTTTAACG-CCTATAAAGTGTCGATACTTTATAACAATGTATC
* * *
1090653 GATCCATAACGATATAACATGAAAAAATATGAC
129 GATCCACAACGATATAACAGGTAAAAATATGAC
* *
1090686 AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTCTCGATACTTTAATATAAGTATCGACACTC
1 AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
* * *
1090751 TATGAATTTAAAAGAAAAGCAGTTTTATCGCCTATAAAGTGTCGATTCTTTATAACAATGTATCG
66 TGTGAATTTAAAAGAAAA-CAGTTTTAACGCCTATAAAGTGTCGATACTTTATAACAATGTATCG
*
1090816 ATCTACAACGATATAACAGGTAAAAATATGAC
130 ATCCACAACGATATAACAGGTAAAAATATGAC
* *
1090848 AAACCCGGTCTCTAAAGAACAAAACCAGTAGAGCGACCGGATATATTGAAAGTGTCGATACTTTA
1 AAAACCGG----TAAAG--------C------GCTACCGGATATATTGAAAGTGTCGATACTTTA
* *
1090913 ATATAA--ATCGACACTTTGTGAATTTAAAAGAGAA-AGTTTTAACGCCTATAAACTGTCGATAC
48 ATATAAGTATCGACACTTTGTGAATTTAAAAGAAAACAGTTTTAACGCCTATAAAGTGTCGATAC
*
1090975 TTTATAACAATGTATTGATCCACAACGATATAACAGGTAAAAATATGAC
113 TTTATAACAATGTATCGATCCACAACGATATAACAGGTAAAAATATGAC
1091024 AAAA
1 AAAA
1091028 TCAGTCTCAA
Statistics
Matches: 296, Mismatches: 26, Indels: 26
0.85 0.07 0.07
Matches are distributed among these distances:
161 5 0.02
162 148 0.50
166 5 0.02
174 1 0.00
176 75 0.25
178 25 0.08
180 37 0.12
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (161 bp):
AAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGTATCGACACTT
TGTGAATTTAAAAGAAAACAGTTTTAACGCCTATAAAGTGTCGATACTTTATAACAATGTATCGA
TCCACAACGATATAACAGGTAAAAATATGAC
Found at i:1091002 original size:176 final size:179
Alignment explanation
Indices: 1090684--1091092 Score: 547
Period size: 176 Copynumber: 2.3 Consensus size: 179
1090674 AAAAAATATG
*
1090684 ACAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTCTCGATACTTTAATATAAGTATCGACAC
1 ACAAAACCAGTAAAGCGC-ACCGGATATATTGAAAGTCTCGATACTTTAATATAAG-ATCGACAC
* * *
1090749 TCTATGAATTTAAAAGAAAAGCAGTTTTATCGCCTATAAAGTGTCGATTCTTTATAACAATGTAT
64 TCTATGAATTTAAAAGAAAA-CAGTTTTAACGCCTATAAACTGTCGATACTTTATAACAATGTAT
*
1090814 CGATCTACAACGATATAACAGGTAAAAATATGACAAACCCGGTCTCTAAAGA
128 CGATCCACAACGATATAACAGGTAAAAATATGACAAACCCGGTCTCTAAAGA
* * *
1090866 ACAAAACCAGTAGAGCG-ACCGGATATATTGAAAGTGTCGATACTTTAATATAA-ATCGACACTT
1 ACAAAACCAGTAAAGCGCACCGGATATATTGAAAGTCTCGATACTTTAATATAAGATCGACACTC
* * *
1090929 TGTGAATTTAAAAGAGAA-AGTTTTAACGCCTATAAACTGTCGATACTTTATAACAATGTATTGA
66 TATGAATTTAAAAGAAAACAGTTTTAACGCCTATAAACTGTCGATACTTTATAACAATGTATCGA
** * * *
1090993 TCCACAACGATATAACAGGTAAAAATATGACAAAATCAGTCTCAAAAGG
131 TCCACAACGATATAACAGGTAAAAATATGACAAACCCGGTCTCTAAAGA
* * * * * * *
1091042 ACAAAA-CGGTAAAGCCCTACCAGATATATTAAAAGTGTTGATATTTTAATA
1 ACAAAACCAGTAAAGCGC-ACCGGATATATTGAAAGTCTCGATACTTTAATA
1091093 AGTACGTGTA
Statistics
Matches: 202, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
175 7 0.03
176 91 0.45
177 29 0.14
178 25 0.12
180 35 0.17
182 15 0.07
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.27
Consensus pattern (179 bp):
ACAAAACCAGTAAAGCGCACCGGATATATTGAAAGTCTCGATACTTTAATATAAGATCGACACTC
TATGAATTTAAAAGAAAACAGTTTTAACGCCTATAAACTGTCGATACTTTATAACAATGTATCGA
TCCACAACGATATAACAGGTAAAAATATGACAAACCCGGTCTCTAAAGA
Found at i:1091878 original size:6 final size:6
Alignment explanation
Indices: 1091867--1091932 Score: 96
Period size: 6 Copynumber: 11.0 Consensus size: 6
1091857 GACACGTATT
* * * *
1091867 ACCACG ACCACG ACCACA ACCACG ACCACG ATCACG ACCACG GCGACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1091915 ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG
1091933 GCGACGAGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
6 52 1.00
ACGTcount: A:0.33, C:0.47, G:0.18, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:1091932 original size:24 final size:24
Alignment explanation
Indices: 1091867--1091939 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 24
1091857 GACACGTATT
** *
1091867 ACCACGACCACGACCACAACCACG
1 ACCACGACCACGACCACGGCGACG
*
1091891 ACCACGATCACGACCACGGCGACG
1 ACCACGACCACGACCACGGCGACG
1091915 ACCACGACCACGACCACGGCGACG
1 ACCACGACCACGACCACGGCGACG
1091939 A
1 A
1091940 GACGGACGGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.33, C:0.45, G:0.21, T:0.01
Consensus pattern (24 bp):
ACCACGACCACGACCACGGCGACG
Found at i:1091939 original size:12 final size:12
Alignment explanation
Indices: 1091900--1091939 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
1091890 GACCACGATC
1091900 ACGACCACGGCG
1 ACGACCACGGCG
* *
1091912 ACGACCACGACC
1 ACGACCACGGCG
1091924 ACGACCACGGCG
1 ACGACCACGGCG
1091936 ACGA
1 ACGA
1091940 GACGGACGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.30, C:0.42, G:0.28, T:0.00
Consensus pattern (12 bp):
ACGACCACGGCG
Found at i:1091954 original size:3 final size:3
Alignment explanation
Indices: 1091946--1092058 Score: 75
Period size: 3 Copynumber: 34.7 Consensus size: 3
1091936 ACGAGACGGA
* *
1091946 CGG CGG CGG CGG CGG CGA CGAG ACGG ACGG C-G CGG CGG CGG CGA CGAG
1 CGG CGG CGG CGG CGG CGG CG-G -CGG -CGG CGG CGG CGG CGG CGG CG-G
* * *
1091994 ACGA CGG CGG CGA CGAG ACGG ACGG CGG CGG CGG CGG CGG CGA CGAG
1 -CGG CGG CGG CGG CG-G -CGG -CGG CGG CGG CGG CGG CGG CGG CG-G
*
1092041 ACGA CGG CGG CGG CGG CG
1 -CGG CGG CGG CGG CGG CG
1092059 CGCGAGAGTC
Statistics
Matches: 89, Mismatches: 12, Indels: 18
0.75 0.10 0.15
Matches are distributed among these distances:
2 2 0.02
3 69 0.78
4 10 0.11
5 8 0.09
ACGTcount: A:0.14, C:0.31, G:0.55, T:0.00
Consensus pattern (3 bp):
CGG
Found at i:1092001 original size:17 final size:17
Alignment explanation
Indices: 1091981--1092052 Score: 91
Period size: 17 Copynumber: 4.5 Consensus size: 17
1091971 GACGGCGCGG
1091981 CGGCGGCGACGAGACGA
1 CGGCGGCGACGAGACGA
1091998 CGGCGGCGACGAGACGGA
1 CGGCGGCGACGAGAC-GA
*
1092016 CGGC-G-G-CG-G-CGG
1 CGGCGGCGACGAGACGA
1092028 CGGCGGCGACGAGACGA
1 CGGCGGCGACGAGACGA
1092045 CGGCGGCG
1 CGGCGGCG
1092053 GCGGCGCGCG
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
12 5 0.11
13 2 0.04
14 2 0.04
15 4 0.09
16 2 0.04
17 26 0.55
18 6 0.13
ACGTcount: A:0.17, C:0.31, G:0.53, T:0.00
Consensus pattern (17 bp):
CGGCGGCGACGAGACGA
Found at i:1092028 original size:47 final size:43
Alignment explanation
Indices: 1091955--1092052 Score: 160
Period size: 47 Copynumber: 2.2 Consensus size: 43
1091945 ACGGCGGCGG
1091955 CGGCGGCGACGAGACGGACGGCGCGGCGGCGGCGACGAGACGA
1 CGGCGGCGACGAGACGGACGGCGCGGCGGCGGCGACGAGACGA
1091998 CGGCGGCGACGAGACGGACGGCGGCGGCGGCGGCGGCGACGAGACGA
1 CGGCGGCGACGAGACGGA---CGGC-GCGGCGGCGGCGACGAGACGA
1092045 CGGCGGCG
1 CGGCGGCG
1092053 GCGGCGCGCG
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
43 18 0.35
46 4 0.08
47 29 0.57
ACGTcount: A:0.16, C:0.31, G:0.53, T:0.00
Consensus pattern (43 bp):
CGGCGGCGACGAGACGGACGGCGCGGCGGCGGCGACGAGACGA
Found at i:1094304 original size:212 final size:205
Alignment explanation
Indices: 1093921--1094329 Score: 730
Period size: 212 Copynumber: 2.0 Consensus size: 205
1093911 GCAGCCAGAG
*
1093921 ATACCTCAAAGGGTGCATAGCAATCTTAGAGGTAATGAGTTGAAGAACGTTTTTGTTTTTTATTG
1 ATACCTCAAAGGGTGCATAGCAATCTTAGAGGTAATGAGTTGAAGAACGTTTTTGTTTTTTATTA
1093986 ATATAATAGTTATTATAAAATTATAAATTTTTATAAATGCAGGTTGCACTGTTCGTTTTTGGTTA
66 ATATAATAGTTATTATAAAATTATAAATTTTTATAAATGCAGGTTGCACTGTTCGTTTTTGGTTA
1094051 GGCTGTGAGGCAGTGCCGGCTAATGAAAGAACCGGAGTGGCACGCATCCGTGCATGGGGGAAGGA
131 GGCTGTGAGGCAGTGCCGGCTAATGAAAGAACCGGAGTGGCACGCATCCGTGCATGGGGGAAGGA
1094116 AGAGGTGGTT
196 AGAGGTGGTT
1094126 ATACCTCAAA-GGTGCATAGCAATCTTAGAGGTAATGAGTTGAAGAACGTTTTTGTTTTTTATAT
1 ATACCTCAAAGGGTGCATAGCAATCTTAGAGGTAATGAGTTGAAGAACGTTTTTGTTTTTTAT-T
1094190 AAAATGATAGTATAGTTATTATAAAATTATAAATTTTATATAAATGCAGGTTGCACTGTTCGATT
65 --AAT-ATA--ATAGTTATTATAAAATTATAAATTTT-TATAAATGCAGGTTGCACTGTTCG-TT
1094255 TTTGGTTAGGCTGTGAGGCAGTGCCGGCTAATGAAAGAACCGGAGTGGCACGCATCCGTGCATGG
123 TTTGGTTAGGCTGTGAGGCAGTGCCGGCTAATGAAAGAACCGGAGTGGCACGCATCCGTGCATGG
1094320 GGGAAGGAAG
188 GGGAAGGAAG
1094330 TGGTTAGAGT
Statistics
Matches: 195, Mismatches: 1, Indels: 9
0.95 0.00 0.04
Matches are distributed among these distances:
204 52 0.27
205 11 0.06
207 2 0.01
208 3 0.02
210 26 0.13
211 24 0.12
212 77 0.39
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (205 bp):
ATACCTCAAAGGGTGCATAGCAATCTTAGAGGTAATGAGTTGAAGAACGTTTTTGTTTTTTATTA
ATATAATAGTTATTATAAAATTATAAATTTTTATAAATGCAGGTTGCACTGTTCGTTTTTGGTTA
GGCTGTGAGGCAGTGCCGGCTAATGAAAGAACCGGAGTGGCACGCATCCGTGCATGGGGGAAGGA
AGAGGTGGTT
Found at i:1094621 original size:21 final size:21
Alignment explanation
Indices: 1094595--1094637 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1094585 CAAAGACAAT
*
1094595 AAAGAGTTGAAGAGAAACTTG
1 AAAGAGTCGAAGAGAAACTTG
* *
1094616 AAAGAGTCGATGAGACACTTG
1 AAAGAGTCGAAGAGAAACTTG
1094637 A
1 A
1094638 GAGGCATAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (21 bp):
AAAGAGTCGAAGAGAAACTTG
Found at i:1096449 original size:19 final size:19
Alignment explanation
Indices: 1096425--1096473 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
1096415 AATGTAGGGT
1096425 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
* *
1096444 TAATTTTGTATACGGTTTA
1 TAATTTTGTATAAGATTTA
1096463 TAATTTTGTAT
1 TAATTTTGTAT
1096474 GTGAATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:1096847 original size:15 final size:15
Alignment explanation
Indices: 1096827--1096868 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
1096817 ATACATTTAT
1096827 AAAAAATATCGATCA
1 AAAAAATATCGATCA
1096842 AAAAAATATCGATCA
1 AAAAAATATCGATCA
*
1096857 AAAAAACATCGA
1 AAAAAATATCGA
1096869 AACCCATAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.62, C:0.14, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAAAATATCGATCA
Found at i:1097292 original size:200 final size:199
Alignment explanation
Indices: 1096842--1097970 Score: 1383
Period size: 198 Copynumber: 5.7 Consensus size: 199
1096832 ATATCGATCA
* ** * ** *
1096842 AAAAAATATCGATCAAAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATAT
1 AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
* * * * * *
1096907 AACCGGTATAAATATACTGGATTTATGTGAGAATAGGTTTACATAATGTATCGACACTTTCT-CA
66 AACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGTACATAATGTATCGACACTTT-TGAA
* * **
1096971 TTTATGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGATGAACGCAT-TTGTGTCGATACA
130 TTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAAGTGTCGATACA
1097035 TTTAT
195 TTTAT
* * *
1097040 AAAAAGTATCGATCCCAGAAACATCGAAACTCATAAATATAATGTAATAGGTAAATTTACAATGT
1 AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
* * * * * *
1097105 AACCGGTATAACTATA-CGGTTTTATGAGAAAATATGTCTACATAATGTATCGAAACGTATGGAA
66 AACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGTACATAATGTATCGACAC-TTTTGAA
* * * *
1097169 TTTGTGTCGATACTGTTTGTCCAGAATGAATGCCCAAAA-GAGTGCACCCATAAAGTGTCAATAC
130 TTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATG-GTGAACGCATAAAGTGTCGATAC
1097233 ATTTAAT
194 ATTT-AT
* * ** *
1097240 AAAAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATAT
1 AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
* * * * * * * *
1097305 AACC-GTATAAATATACCAGTTTTATGTGAGAATATGTATACATAATGTGTCGACATTTTTTAAT
66 AACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGTACATAATGTATCGACACTTTTGAA-
* * *
1097369 TTTGTGTCGATACTTTTT-TCCAAAATGAATGCCCAAAATGGTGAACGCGTAAAGTGTCTATACA
130 TTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAAGTGTCGATACA
1097433 TTTAT
195 TTTAT
* * *
1097438 AAAAAATATCGATCCCAAAAATATCG-AACCGATAA-T-TAATGTAATAGGTAAATTTACAATGT
1 AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
* * * * *
1097500 -A-CGGTAT-AATATACCGATTTTATGTGAGAATAGGTGTACATAATGTGTCGATAC-TTTGAAT
66 AACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGTACATAATGTATCGACACTTTTGAAT
1097561 TTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAAGTGTCGATACAT
131 TTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAAGTGTCGATACAT
1097626 TTAT
196 TTAT
* * * * *
1097630 AAAAAGTTTTGATCCAAAAAATATCGAAACCAATAATTATAATGTAATAGGTAAATTTACAATGT
1 AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
* * * * * *
1097695 AACCAGTATAAATATACTGGTTTTATGAGAAAATAAAG-GAACATAATGTGTCGACACTTTTTAA
66 AACCGGTATAAATATACCGGTTTTATGAGAAAAT-AGGTGTACATAATGTATCGACAC-TTTTGA
* *
1097759 ATTTGTGTCGATACTTTTTGTCCAGAATAAATGCCCAAAATGGTGAACACATAAAGTGTCGATAC
129 ATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAAGTGTCGATAC
**
1097824 ATACAT
194 ATTTAT
* *
1097830 AAAAAGTATCGATCCCAAAAACATCG-AACCGATAATTATAATGTAATAGGTAAA-TTACATTGT
1 AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
* * *
1097893 AACCGATATAAATTTACCGGTTTTATGAGAAAATAGGTGAACATAATGTATCGACACGTTTT-AG
66 AACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGTACATAATGTATCGACAC-TTTTGA-
*
1097957 ATTTGTATCGATAC
129 ATTTGTGTCGATAC
1097971 AATTTTAAAT
Statistics
Matches: 806, Mismatches: 104, Indels: 42
0.85 0.11 0.04
Matches are distributed among these distances:
191 18 0.02
192 75 0.09
193 50 0.06
194 6 0.01
195 48 0.06
196 2 0.00
197 50 0.06
198 252 0.31
199 98 0.12
200 207 0.26
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (199 bp):
AAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGT
AACCGGTATAAATATACCGGTTTTATGAGAAAATAGGTGTACATAATGTATCGACACTTTTGAAT
TTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCATAAAGTGTCGATACAT
TTAT
Found at i:1099498 original size:15 final size:15
Alignment explanation
Indices: 1099471--1099514 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
1099461 GATGAAGAAG
*
1099471 ATGATGATGATGATT
1 ATGATTATGATGATT
* *
1099486 ATTATTATTATGATT
1 ATGATTATGATGATT
1099501 ATGATTATGATGAT
1 ATGATTATGATGAT
1099515 CCAAACAAGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.48
Consensus pattern (15 bp):
ATGATTATGATGATT
Found at i:1100870 original size:24 final size:24
Alignment explanation
Indices: 1100819--1100871 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
1100809 TTTCATATGT
* * *
1100819 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
* *
1100843 AATTTGAGTTTGAGTTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
1100867 AATTT
1 AATTT
1100872 CGGATTCACT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:1102158 original size:199 final size:199
Alignment explanation
Indices: 1101298--1102193 Score: 1165
Period size: 200 Copynumber: 4.5 Consensus size: 199
1101288 CGATACTGAA
* * * *** *
1101298 AAATTTACAATGGAACCAATATAAATATACCGGTTTTTTTGAGAAAATAGACATACATAATGTAT
1 AAATTTACAATGTAACCAGTATAAATATACCGG-TTTTATGAGAAAATAGGTGTACATAATGTGT
* * * * * ** * * *
1101363 CAAAACTTGTGGAATTTGTGTCGATAC-TTTTGATCTACGAGGAATGCCCAAATAGGGTGCACCC
65 CGACACTTTTAG-ATTTGTGTCGATACTTTTTG-TCCAAAATGAATGCCCAAA-AGGGTGAACGC
* * * *
1101427 ATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAATATCGAAACAAATAATTATAATA
127 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATG
*
1101492 TAATAAGT
192 TAATAGGT
* * * *
1101500 AAATTTACAATGTAACCAATATAAATATACCGGTTTTATGTGAGAATATGTGTACATAATGTGTC
1 AAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTGTACATAATGTGTC
* * *
1101565 GACACTTTT-GAATTTTGTATCAATACTTTTTGTCCAAAATGAATGCCCAAAATGGTGAACGCAT
66 GACACTTTTAG-A-TTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAAAGGGTGAACGCAT
*
1101629 AAAGTGTCGATACATTTATAAAAAGTATCGATCCTAAAAACATCGAAACCAATAATTATAATGTA
129 AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTA
1101694 ATAGGT
194 ATAGGT
* * *
1101700 AAATTTACAATGTAACCAGTATTAATATACCGGTTTTATGAGAAAATAGG-GAAACATAATATGT
1 AAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTG-TACATAATGTGT
* * *
1101764 CGACACTTTTTAAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCCAAAATGGTGAACGCAT
65 CGACAC-TTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAAAGGGTGAACGCAT
*
1101829 AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAATCAATAATTATAATGTA
129 AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTA
1101894 ATAGGT
194 ATAGGT
* * * * *
1101900 AAATTTACAATGTAATCAGTATAAATGTACCGGTTTTATGAGAAAATATGTGAACATAATGTATC
1 AAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTGTACATAATGTGTC
1101965 GACACATTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATG-CCAAAAGGGTTGCAA-GCA
66 GACAC-TTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAAAGGG-TG-AACGCA
* * * * * *
1102028 TAAAGT-TCGATATATTTTTAAAAAGAAACGATCCCAAAAACATTGAAACCGATAATTATAATGT
128 TAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGT
1102092 AATAGGT
193 AATAGGT
* * * *
1102099 AAATTTACAATGTAATCGGTATAAATATACCGATTTTATGAGAGAATAGGTGTACATAATGTGTC
1 AAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTGTACATAATGTGTC
*
1102164 GACACTTTTGGATTTTGTGTCGATACTTTT
66 GACACTTTTAGA-TTTGTGTCGATACTTTT
1102194 AAATAACGCA
Statistics
Matches: 620, Mismatches: 65, Indels: 21
0.88 0.09 0.03
Matches are distributed among these distances:
198 6 0.01
199 147 0.24
200 366 0.59
201 64 0.10
202 37 0.06
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (199 bp):
AAATTTACAATGTAACCAGTATAAATATACCGGTTTTATGAGAAAATAGGTGTACATAATGTGTC
GACACTTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCCAAAAGGGTGAACGCATAA
AGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCAATAATTATAATGTAAT
AGGT
Found at i:1106753 original size:199 final size:197
Alignment explanation
Indices: 1106309--1107021 Score: 805
Period size: 199 Copynumber: 3.6 Consensus size: 197
1106299 ATATTCGTCA
*
1106309 ATACATTT-TCTAAAAGTATCGA-CCCAAAAAACATCGAAACCAATAATTATAATGTAATAGGTA
1 ATACATTTAT-TAAAAGTATCGATCCC-AAAAACATCGAAACCGATAATTATAATGTAATAGGTA
* * * * * * *
1106372 AATTAACAATGTAACCGGTATAAATATACTGGTTAATTAGAAAACAGGTAAACATAATGTATCGA
64 AATTTACAATGTAACCGGTATAAATATAC-GTTTTATGAGAAAATAGGTCATCATAATGTATCGA
* *
1106437 CACTTGTGT-AATTTGTGTCGATACTTATTGTCCAGAATGAATGCTCAAACGAGGTACACGCATA
128 CACTTGT-TAAATTTGTGTCGATACTT-TTGTCCAAAATGAATGC-CAAACGAGGTGCACGCATA
1106501 AAGTGTCG
190 AAGTGTCG
* * * * *
1106509 ATACAATTATTAAAAGTATCGATCCCAATAAA-ATTGAATCCGATAATTATAATGTAACATGTAA
1 ATACATTTATTAAAAGTATCGATCCCAA-AAACATCGAAACCGATAATTATAATGTAATAGGTAA
*
1106573 ATTTACAATGTAACCGGTATAAATATATCGATTTTATGAGAAAATAGGTCATCATAAAGTATCGA
65 ATTTACAATGTAACCGGTATAAATATA-CG-TTTTATGAGAAAATAGGTCATCATAATGTATCGA
* *
1106638 CACTTGTTAAATTTTTGTCGATACATTTTGTCCATAATGAATGCCAAACG-GGTGCACGCATAAA
128 CACTTGTTAAATTTGTGTCGATAC-TTTTGTCCAAAATGAATGCCAAACGAGGTGCACGCATAAA
1106702 GTGTCG
192 GTGTCG
* * *
1106708 ATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAAATACAATGTGATAGGTAAA
1 ATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAA
* * * * * *
1106773 TTTACAATGTACCCGATAGAAATATACCCGTTTTATGAAAAAAATATGTC-TAAATAATGTATCG
66 TTTACAATGTAACCGGTATAAATATA--CGTTTTATG-AGAAAATAGGTCAT-CATAATGTATCG
* * * * *
1106837 ACACTCT-TTAAGTTTGTGTCGATACTTTTTTCCAAAATGAGTGCCCAACGAGGTGCACACATAA
127 ACACT-TGTTAAATTTGTGTCGATACTTTTGTCCAAAATGAATGCCAAACGAGGTGCACGCATAA
1106901 AGTGTCG
191 AGTGTCG
* ** * * *
1106908 ATACATTTA--AAATTGTATTAATCCAAAAAACATTGAAACCGATAATTATAATGTAATAGATAA
1 ATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAA
* * * * * *
1106971 ATTTGCAATATTACCGGTATAAATATACCGGTTTACTTATAAAATAGGTCA
65 ATTTACAATGTAACCGGTATAAATATA-CGTTTTA-TGAGAAAATAGGTCA
1107022 ATATAAGCGC
Statistics
Matches: 438, Mismatches: 59, Indels: 33
0.83 0.11 0.06
Matches are distributed among these distances:
198 23 0.05
199 187 0.43
200 153 0.35
201 73 0.17
202 2 0.00
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (197 bp):
ATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAA
TTTACAATGTAACCGGTATAAATATACGTTTTATGAGAAAATAGGTCATCATAATGTATCGACAC
TTGTTAAATTTGTGTCGATACTTTTGTCCAAAATGAATGCCAAACGAGGTGCACGCATAAAGTGT
CG
Found at i:1107051 original size:23 final size:23
Alignment explanation
Indices: 1107022--1107069 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
1107012 AAATAGGTCA
* *
1107022 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGATACCTAATACATT
*
1107045 ATATAAGCGATACCTAATATATT
1 ATATAAGCGATACCTAATACATT
1107068 AT
1 AT
1107070 TGTACTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGATACCTAATACATT
Found at i:1107156 original size:23 final size:23
Alignment explanation
Indices: 1107106--1107150 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1107096 TGCCTATTTT
* * *
1107106 ATTATATAATCGCTACCTATTAC
1 ATTATATAAGCGATACCTAATAC
1107129 ATTATATAAGCGATACCTAATA
1 ATTATATAAGCGATACCTAATA
1107151 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGATACCTAATAC
Found at i:1107243 original size:23 final size:23
Alignment explanation
Indices: 1107193--1107237 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1107183 TGCCTATTTT
*
1107193 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
1107216 ATTATATAAGCGCTATCTAATA
1 ATTATATAAGCGCTACCTAATA
1107238 TGTTATTGTA
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:0.38, C:0.18, G:0.09, T:0.36
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1107271 original size:87 final size:87
Alignment explanation
Indices: 1107022--1107260 Score: 433
Period size: 87 Copynumber: 2.7 Consensus size: 87
1107012 AAATAGGTCA
*
1107022 ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATATTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTACTTGATAATATTT
1107087 CTGGTTAAATGCCTATTTTATT
66 CTGGTTAAATGCCTATTTTATT
*
1107109 ATATAATCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTACTTGATAATATTT
1107174 CTGGTTAAATGCCTATTTTATT
66 CTGGTTAAATGCCTATTTTATT
* * *
1107196 ATATAAGCGCTACCTATTACATTATATAAGCGCTATCTAATATGTTATTGTACTTAATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTACTTGATAATATTT
1107261 TCGATTAAAT
Statistics
Matches: 146, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 146 1.00
ACGTcount: A:0.33, C:0.14, G:0.10, T:0.43
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATGTTATTGTACTTGATAATATTT
CTGGTTAAATGCCTATTTTATT
Found at i:1111607 original size:22 final size:22
Alignment explanation
Indices: 1111582--1111632 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
1111572 TCCACATCAT
1111582 CACATTGTTTGGATTTTAACAA
1 CACATTGTTTGGATTTTAACAA
1111604 CACATTGTTTGGATTTTAACAA
1 CACATTGTTTGGATTTTAACAA
1111626 CACATTG
1 CACATTG
1111633 CTCTAATTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (22 bp):
CACATTGTTTGGATTTTAACAA
Found at i:1118897 original size:8 final size:8
Alignment explanation
Indices: 1118862--1118922 Score: 52
Period size: 8 Copynumber: 7.6 Consensus size: 8
1118852 AAACAGACCT
1118862 AATGATCG
1 AATGATCG
1118870 AATGA-CG
1 AATGATCG
* * *
1118877 TAATAACCT
1 -AATGATCG
1118886 AATGATCG
1 AATGATCG
*
1118894 AATGACCG
1 AATGATCG
* *
1118902 AATAATTG
1 AATGATCG
1118910 AATGATCG
1 AATGATCG
1118918 AATGA
1 AATGA
1118923 CCTATTAAAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
7 2 0.05
8 37 0.93
9 1 0.03
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.25
Consensus pattern (8 bp):
AATGATCG
Found at i:1118924 original size:24 final size:25
Alignment explanation
Indices: 1118858--1118924 Score: 95
Period size: 24 Copynumber: 2.8 Consensus size: 25
1118848 ATTCAAACAG
1118858 ACCTAATGATCGAATGA-CGTAATA
1 ACCTAATGATCGAATGACCGTAATA
1118882 ACCTAATGATCGAATGACCG-AATA
1 ACCTAATGATCGAATGACCGTAATA
*
1118906 A-TTGAATGATCGAATGACC
1 ACCT-AATGATCGAATGACC
1118925 TATTAAAATC
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
23 1 0.03
24 37 0.93
25 2 0.05
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (25 bp):
ACCTAATGATCGAATGACCGTAATA
Found at i:1125097 original size:16 final size:17
Alignment explanation
Indices: 1125058--1125097 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1125048 AATTTTTTGT
1125058 ATTATTTTTAGAAAAAA
1 ATTATTTTTAGAAAAAA
* *
1125075 ATAATTTTTAG-ACAAA
1 ATTATTTTTAGAAAAAA
1125091 ATTATTT
1 ATTATTT
1125098 AATAACTGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (17 bp):
ATTATTTTTAGAAAAAA
Found at i:1125208 original size:20 final size:20
Alignment explanation
Indices: 1125185--1125222 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1125175 TTAAAAAATA
1125185 TTTTAATAATAATTATAATT
1 TTTTAATAATAATTATAATT
**
1125205 TTTTAATTGTAATTATAA
1 TTTTAATAATAATTATAA
1125223 ATGTACCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (20 bp):
TTTTAATAATAATTATAATT
Found at i:1125255 original size:2 final size:2
Alignment explanation
Indices: 1125248--1125279 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1125238 GTACGCTTTC
1125248 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
1125280 TTTAAACGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1125621 original size:15 final size:15
Alignment explanation
Indices: 1125580--1125622 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 15
1125570 AATCAAGTAG
* *
1125580 TTTTGAAATATATAT
1 TTTTTAAATATTTAT
*
1125595 TTTATAAA-ATTTAT
1 TTTTTAAATATTTAT
1125609 TTTTTAAATATTTA
1 TTTTTAAATATTTA
1125623 AAATAATTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTTTAAATATTTAT
Found at i:1127388 original size:20 final size:20
Alignment explanation
Indices: 1127359--1127412 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
1127349 AAAATGAATT
* * **
1127359 GTATCAATACCCTAAATGTA
1 GTATCGATACCCCAAATCAA
*
1127379 GTATCGATACCCCCAATCAA
1 GTATCGATACCCCAAATCAA
1127399 GTATCGATACCCCA
1 GTATCGATACCCCA
1127413 TTGAGTATCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.24
Consensus pattern (20 bp):
GTATCGATACCCCAAATCAA
Found at i:1128109 original size:13 final size:13
Alignment explanation
Indices: 1128091--1128127 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1128081 CTATGGTACT
1128091 TGGAGAGGAAAGA
1 TGGAGAGGAAAGA
*
1128104 TGGAGATGAAA-A
1 TGGAGAGGAAAGA
1128116 TGG-GAGGAAAGA
1 TGGAGAGGAAAGA
1128128 GAATATTAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
11 6 0.29
12 5 0.24
13 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.43, T:0.11
Consensus pattern (13 bp):
TGGAGAGGAAAGA
Found at i:1130036 original size:27 final size:26
Alignment explanation
Indices: 1130002--1130057 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 26
1129992 TTAATTTGTG
1130002 TTTTAATTAAATGGT-TTTTTAATTTAA
1 TTTTAATTAAAT--TCTTTTTAATTTAA
* *
1130029 TTTTAATTTAATTCTTTTTAATTTTA
1 TTTTAATTAAATTCTTTTTAATTTAA
1130055 TTT
1 TTT
1130058 ATTTTCTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.04
26 14 0.54
27 11 0.42
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTTAATTAAATTCTTTTTAATTTAA
Found at i:1130038 original size:16 final size:15
Alignment explanation
Indices: 1130019--1130062 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1130009 TAAATGGTTT
1130019 TTTAATTTAATTTTAA
1 TTTAATTT-ATTTTAA
1130035 TTTAATTCT-TTTTAA
1 TTTAATT-TATTTTAA
*
1130050 TTTTATTTATTTT
1 TTTAATTTATTTT
1130063 CTTCATTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.04
15 16 0.64
16 7 0.28
17 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTAATTTATTTTAA
Found at i:1130048 original size:21 final size:19
Alignment explanation
Indices: 1130024--1130075 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
1130014 GGTTTTTTAA
1130024 TTTAATTTTAATTTAATTCTT
1 TTTAATTTTAATTT-ATT-TT
1130045 TTTAATTTT-ATTTATTTT
1 TTTAATTTTAATTTATTTT
* *
1130063 CTTCATTTTAATT
1 TTTAATTTTAATT
1130076 GTTTTTAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 9 0.32
19 6 0.21
20 4 0.14
21 9 0.32
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTAATTTTAATTTATTTT
Found at i:1130102 original size:15 final size:15
Alignment explanation
Indices: 1130084--1130129 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
1130074 TTGTTTTTAA
1130084 TCTTATTTTTTTATT
1 TCTTATTTTTTTATT
*
1130099 TCTTA-TTTCTTATT
1 TCTTATTTTTTTATT
1130113 T-TTACTTCTTTTTATT
1 TCTTA-TT-TTTTTATT
1130129 T
1 T
1130130 TTTAAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 3 0.12
14 9 0.35
15 6 0.23
16 8 0.31
ACGTcount: A:0.13, C:0.11, G:0.00, T:0.76
Consensus pattern (15 bp):
TCTTATTTTTTTATT
Found at i:1135154 original size:21 final size:21
Alignment explanation
Indices: 1135128--1135172 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1135118 GATTTCTGGG
* *
1135128 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1135149 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1135170 CAA
1 CAA
1135173 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1136013 original size:31 final size:31
Alignment explanation
Indices: 1135975--1136068 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
1135965 AGGGTCGAGG
1135975 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
1136006 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
1136037 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
1136068 G
1 G
1136069 GTCCTTCGGG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 56 0.98
32 1 0.02
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:1137586 original size:9 final size:10
Alignment explanation
Indices: 1137555--1137590 Score: 56
Period size: 11 Copynumber: 3.6 Consensus size: 10
1137545 AACGCTGGAA
1137555 ACCGGTTTTG
1 ACCGGTTTTG
1137565 AACCGGTTTTG
1 -ACCGGTTTTG
1137576 ACCGG-TTTG
1 ACCGGTTTTG
1137585 ACCGGT
1 ACCGGT
1137591 CACGACCCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 9 0.38
10 5 0.21
11 10 0.42
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1137608 original size:23 final size:22
Alignment explanation
Indices: 1137582--1137636 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
1137572 TTTGACCGGT
* * *
1137582 TTGACCGGTCACGACCCGACCCG
1 TTGACCCGACACGACCCGA-CAG
*
1137605 TTGACCCGACCCGACCCGACAG
1 TTGACCCGACACGACCCGACAG
1137627 TTGACCCGAC
1 TTGACCCGAC
1137637 CCGTTGACCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 12 0.43
23 16 0.57
ACGTcount: A:0.20, C:0.44, G:0.24, T:0.13
Consensus pattern (22 bp):
TTGACCCGACACGACCCGACAG
Found at i:1137612 original size:13 final size:13
Alignment explanation
Indices: 1137594--1137645 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
1137584 GACCGGTCAC
1137594 GACCCGACCCGTT
1 GACCCGACCCGTT
1137607 GACCCGACCC---
1 GACCCGACCCGTT
*
1137617 GACCCGA-CAGTT
1 GACCCGACCCGTT
1137629 GACCCGACCCGTT
1 GACCCGACCCGTT
1137642 GACC
1 GACC
1137646 GGTGCTATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 1 0.03
10 7 0.21
12 7 0.21
13 18 0.55
ACGTcount: A:0.19, C:0.46, G:0.23, T:0.12
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1137632 original size:22 final size:23
Alignment explanation
Indices: 1137593--1137639 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
1137583 TGACCGGTCA
*
1137593 CGACCCGACCCGTTGACCCGACC
1 CGACCCGACCAGTTGACCCGACC
1137616 CGACCCGA-CAGTTGACCCGACC
1 CGACCCGACCAGTTGACCCGACC
1137638 CG
1 CG
1137640 TTGACCGGTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.19, C:0.49, G:0.23, T:0.09
Consensus pattern (23 bp):
CGACCCGACCAGTTGACCCGACC
Found at i:1144836 original size:9 final size:10
Alignment explanation
Indices: 1144786--1144833 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
1144776 AACGCTGGAA
1144786 ACCGGTTTTG
1 ACCGGTTTTG
*
1144796 ACCGG-TTTA
1 ACCGGTTTTG
1144805 ACCGGTTTTG
1 ACCGGTTTTG
*
1144815 AACAGGTTTTG
1 -ACCGGTTTTG
1144826 ACCGGTTT
1 ACCGGTTT
1144834 GACTGGTCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 15 0.47
11 9 0.28
ACGTcount: A:0.17, C:0.19, G:0.27, T:0.38
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:1144874 original size:17 final size:18
Alignment explanation
Indices: 1144843--1144884 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
1144833 TGACTGGTCA
1144843 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
1144861 CGACCCGA-CCGTTGACC
1 CGACCCGACCCGTTGACC
1144878 CGACCCG
1 CGACCCG
1144885 TTGACCGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.17, C:0.50, G:0.24, T:0.10
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:1144879 original size:12 final size:13
Alignment explanation
Indices: 1144844--1144890 Score: 58
Period size: 13 Copynumber: 3.3 Consensus size: 13
1144834 GACTGGTCAC
1144844 GACCCGACCCGTT
1 GACCCGACCCGTT
1144857 GACCCGACCCGACCGTT
1 GACCCGA--C--CCGTT
1144874 GACCCGACCCGTT
1 GACCCGACCCGTT
1144887 GACC
1 GACC
1144891 GGTGCTATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
13 16 0.53
15 2 0.07
17 12 0.40
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1144953 original size:29 final size:29
Alignment explanation
Indices: 1144921--1144987 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
1144911 TTTGATTTTA
*
1144921 GTGCTATTTTGGGAATTAATTCGAAAAGG
1 GTGCTATTTTGGGAATTAATTCAAAAAGG
* * * *
1144950 GTGCTATATTGGTAATTATTTTAAAAAGG
1 GTGCTATTTTGGGAATTAATTCAAAAAGG
1144979 GTGCTATTT
1 GTGCTATTT
1144988 GTGTAAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (29 bp):
GTGCTATTTTGGGAATTAATTCAAAAAGG
Found at i:1154673 original size:22 final size:21
Alignment explanation
Indices: 1154648--1154695 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
1154638 TTAATTTGCG
1154648 TTTTAATTAAATGAT-TTTTTAA
1 TTTTAATTAAAT--TCTTTTTAA
* *
1154670 TTTTATTTTAATTCTTTTTAA
1 TTTTAATTAAATTCTTTTTAA
1154691 TTTTA
1 TTTTA
1154696 TTTATTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 12 0.52
22 10 0.43
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTAATTAAATTCTTTTTAA
Done.