Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008122.1 Hibiscus syriacus cultivar Beakdansim tig00110676_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: 2511854
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 8
Found at i:884827 original size:28 final size:28
Alignment explanation
Indices: 884767--884825 Score: 91
Period size: 29 Copynumber: 2.1 Consensus size: 28
884757 GTTCACACCT
* *
884767 AAATTAATTTGATGTTATTGCTTACATC
1 AAATTAATTTAATGTCATTGCTTACATC
884795 AAATTAATTTTAATGTCATTGCTTACATC
1 AAATTAA-TTTAATGTCATTGCTTACATC
884824 AA
1 AA
884826 TTTAGTTAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (28 bp):
AAATTAATTTAATGTCATTGCTTACATC
Found at i:889477 original size:29 final size:28
Alignment explanation
Indices: 889438--889497 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 28
889428 CACACCTAAA
889438 TTAATTTGATGTCATTGCTTACATCAAT
1 TTAATTTGATGTCATTGCTTACATCAAT
889466 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAA-TTTGATGTCATTGCTTACATCAAT
889495 TTA
1 TTA
889498 GTTAGGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.48
Consensus pattern (28 bp):
TTAATTTGATGTCATTGCTTACATCAAT
Found at i:892641 original size:31 final size:31
Alignment explanation
Indices: 892583--892641 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
892573 CTATAGTGAC
**
892583 CACATCTTAATTAAAACAAAATGAAAGTCAT
1 CACATCTTAATTAAAACAAAACCAAAGTCAT
*
892614 CACATCTTAATTAAATCAAAACCAAAGT
1 CACATCTTAATTAAAACAAAACCAAAGT
892642 GACCAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.51, C:0.19, G:0.05, T:0.25
Consensus pattern (31 bp):
CACATCTTAATTAAAACAAAACCAAAGTCAT
Found at i:893194 original size:55 final size:55
Alignment explanation
Indices: 893110--893215 Score: 160
Period size: 55 Copynumber: 1.9 Consensus size: 55
893100 AATATTACAC
* * *
893110 ATAAGTACTAAGAGGTGGTCACAACTATTAATCTAAACAGAATTATTTGATTGGT
1 ATAAGTACTAAGAAGTGGTCACAACTATTAATCTAAACAAAATTATATGATTGGT
*
893165 ATAAGTACT-AGAAAGTGGTCACAACTATTATTCTAAACAAAATTATATGAT
1 ATAAGTACTAAG-AAGTGGTCACAACTATTAATCTAAACAAAATTATATGAT
893216 GGTGATTTGC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 2 0.04
55 44 0.96
ACGTcount: A:0.42, C:0.11, G:0.15, T:0.32
Consensus pattern (55 bp):
ATAAGTACTAAGAAGTGGTCACAACTATTAATCTAAACAAAATTATATGATTGGT
Found at i:906097 original size:20 final size:20
Alignment explanation
Indices: 906072--906112 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
906062 GCAAAGTCTG
*
906072 GATACCCGGACTTTGGTTTT
1 GATACCCGGACATTGGTTTT
906092 GATACCCGGACATTGGTTTT
1 GATACCCGGACATTGGTTTT
906112 G
1 G
906113 GCATGTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.27, T:0.37
Consensus pattern (20 bp):
GATACCCGGACATTGGTTTT
Found at i:911718 original size:15 final size:15
Alignment explanation
Indices: 911694--911725 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
911684 CCTTATTTCG
911694 ACATTGTCTTAAATA
1 ACATTGTCTTAAATA
*
911709 ACATTTTCTTAAATA
1 ACATTGTCTTAAATA
911724 AC
1 AC
911726 TTTCTCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.41
Consensus pattern (15 bp):
ACATTGTCTTAAATA
Found at i:911852 original size:23 final size:24
Alignment explanation
Indices: 911826--911871 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
911816 TCTTTGTGAC
911826 ACGTTTATC-TTTGTCTTT-TTGGA
1 ACGTTTATCGTTT-TCTTTCTTGGA
*
911849 ACGTTTTTCGTTTTCTTTCTTGG
1 ACGTTTATCGTTTTCTTTCTTGG
911872 TTGTTTGGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.09, C:0.15, G:0.17, T:0.59
Consensus pattern (24 bp):
ACGTTTATCGTTTTCTTTCTTGGA
Found at i:914870 original size:186 final size:190
Alignment explanation
Indices: 914615--914985 Score: 696
Period size: 192 Copynumber: 2.0 Consensus size: 190
914605 AAATTATACA
914615 TCAAACACAAACCTTAAACAAGGGAACTGAAATTTTGCAAGAAAAATTTTAGATTTTGAGTCCCA
1 TCAAACACAAACCTTAAACAAGGGAACTGAAATTTTGCAAGAAAAATTTTAGATTTTGAGTCCCA
914680 TAGGAACATCATTTATTT-AGC-A-A-TAGTATATGTCTTCAAAATACATCTGATCTCATCGCCT
66 TAGGAACATCATTTATTTAAGCAATAGTAGTATATGTCTTCAAAATACATCTGATCTCATCGCCT
914741 CAAAACAATGAGCCTGGAATGCCTTGATCGTCATGGCAGCAAACGAAAGATGTAGTCTCC
131 CAAAACAATGAGCCTGGAATGCCTTGATCGTCATGGCAGCAAACGAAAGATGTAGTCTCC
914801 TCAAACACAAACCTTAAACAAGGGAACTGAAATTTTGCAAGAAAAATTTTAGATTTTGAGTCCCA
1 TCAAACACAAACCTTAAACAAGGGAACTGAAATTTTGCAAGAAAAATTTTAGATTTTGAGTCCCA
914866 TAGGAACATCATTTATTTAGCAGCAATAGTAGTATATGTCTTCAAAATACATCTGATCTCATCGC
66 TAGGAACATCATTTATTTA--AGCAATAGTAGTATATGTCTTCAAAATACATCTGATCTCATCGC
914931 CTCAAAACAATGAGCCTGGAATGCCTTGATCGTCATGGCAGCAAACGAAAGATGT
129 CTCAAAACAATGAGCCTGGAATGCCTTGATCGTCATGGCAGCAAACGAAAGATGT
914986 GTATGTCTCC
Statistics
Matches: 179, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
186 83 0.46
189 3 0.02
190 1 0.01
191 1 0.01
192 91 0.51
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.27
Consensus pattern (190 bp):
TCAAACACAAACCTTAAACAAGGGAACTGAAATTTTGCAAGAAAAATTTTAGATTTTGAGTCCCA
TAGGAACATCATTTATTTAAGCAATAGTAGTATATGTCTTCAAAATACATCTGATCTCATCGCCT
CAAAACAATGAGCCTGGAATGCCTTGATCGTCATGGCAGCAAACGAAAGATGTAGTCTCC
Found at i:923318 original size:17 final size:17
Alignment explanation
Indices: 923298--923350 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
923288 TGTAATGTTT
923298 TTTATTTAATGTTTCTA
1 TTTATTTAATGTTTCTA
* *
923315 TTTAATT--T-TTT-AA
1 TTTATTTAATGTTTCTA
*
923328 TGTATTTAATGTTTCTA
1 TTTATTTAATGTTTCTA
923345 TTTATT
1 TTTATT
923351 ATTTAGATTG
Statistics
Matches: 26, Mismatches: 6, Indels: 8
0.65 0.15 0.20
Matches are distributed among these distances:
13 6 0.23
14 3 0.12
15 2 0.08
16 3 0.12
17 12 0.46
ACGTcount: A:0.25, C:0.04, G:0.06, T:0.66
Consensus pattern (17 bp):
TTTATTTAATGTTTCTA
Found at i:923353 original size:50 final size:50
Alignment explanation
Indices: 923254--923355 Score: 118
Period size: 50 Copynumber: 2.0 Consensus size: 50
923244 GTTTGAATTG
* * * * *
923254 TAATGTTTGTATTTATTTTTTTTATTATTTAATTTGTAATGTTTTTTATT
1 TAATGTTTCTATTTAATTTTTTAATTATTTAATTTGTAATATTTATTATT
*
923304 TAATGTTTCTATTTAATTTTTTAATGTATTTAATGTT-T-CTATTTATTATT
1 TAATGTTTCTATTTAATTTTTTAAT-TATTTAAT-TTGTAATATTTATTATT
923354 TA
1 TA
923356 GATTGTATAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
50 33 0.75
51 9 0.20
52 2 0.05
ACGTcount: A:0.25, C:0.02, G:0.07, T:0.67
Consensus pattern (50 bp):
TAATGTTTCTATTTAATTTTTTAATTATTTAATTTGTAATATTTATTATT
Found at i:924711 original size:16 final size:16
Alignment explanation
Indices: 924690--924725 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
924680 TTGAGAGATG
924690 TAGTAGATGAAATTTT
1 TAGTAGATGAAATTTT
924706 TAGTAGATGAAATTTT
1 TAGTAGATGAAATTTT
924722 TAGT
1 TAGT
924726 TTTGAGTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.44
Consensus pattern (16 bp):
TAGTAGATGAAATTTT
Found at i:933236 original size:72 final size:72
Alignment explanation
Indices: 933115--933258 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
933105 CCAAATTTGC
* * *
933115 CTCCGTGCTTATTGTACGAAGCATCATTTATAGTCAACATATTGCTTATTTTTCAATTATTTTGC
1 CTCCGTGCTTATTGTACGAAGCATCATATATAGTCAACATATTGATTATTTCTCAATTATTTTGC
933180 TAATTGT
66 TAATTGT
*
933187 CTCCGTGCTTATTGTATGAAGCATCATATATAGTCAACATATTGATTATTTCTCAATTATTTTGC
1 CTCCGTGCTTATTGTACGAAGCATCATATATAGTCAACATATTGATTATTTCTCAATTATTTTGC
933252 TAATTGT
66 TAATTGT
933259 TCTCGTCTCG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.45
Consensus pattern (72 bp):
CTCCGTGCTTATTGTACGAAGCATCATATATAGTCAACATATTGATTATTTCTCAATTATTTTGC
TAATTGT
Found at i:947631 original size:144 final size:144
Alignment explanation
Indices: 947371--947656 Score: 572
Period size: 144 Copynumber: 2.0 Consensus size: 144
947361 ATTTCGTAAC
947371 AGGATTACCAATGACACTGAATAAAAAAGACTCAATTTGGGTGATAGTTGATAAACTGACCAAGA
1 AGGATTACCAATGACACTGAATAAAAAAGACTCAATTTGGGTGATAGTTGATAAACTGACCAAGA
947436 CATCACATTTCATCCATGTTTGGACTGACTACTCGATAGACAAGTATGCAAAGTTATACATCATG
66 CATCACATTTCATCCATGTTTGGACTGACTACTCGATAGACAAGTATGCAAAGTTATACATCATG
947501 GAGATAATTCGAAA
131 GAGATAATTCGAAA
947515 AGGATTACCAATGACACTGAATAAAAAAGACTCAATTTGGGTGATAGTTGATAAACTGACCAAGA
1 AGGATTACCAATGACACTGAATAAAAAAGACTCAATTTGGGTGATAGTTGATAAACTGACCAAGA
947580 CATCACATTTCATCCATGTTTGGACTGACTACTCGATAGACAAGTATGCAAAGTTATACATCATG
66 CATCACATTTCATCCATGTTTGGACTGACTACTCGATAGACAAGTATGCAAAGTTATACATCATG
947645 GAGATAATTCGA
131 GAGATAATTCGA
947657 TTACAAGGGG
Statistics
Matches: 142, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 142 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (144 bp):
AGGATTACCAATGACACTGAATAAAAAAGACTCAATTTGGGTGATAGTTGATAAACTGACCAAGA
CATCACATTTCATCCATGTTTGGACTGACTACTCGATAGACAAGTATGCAAAGTTATACATCATG
GAGATAATTCGAAA
Found at i:948455 original size:26 final size:26
Alignment explanation
Indices: 948423--948497 Score: 114
Period size: 26 Copynumber: 2.8 Consensus size: 26
948413 ATACATTAGG
948423 AAATACTAATTTATAATATTTATTAA
1 AAATACTAATTTATAATATTTATTAA
* *
948449 AAGTACTATTTTATAATATTTATTAA
1 AAATACTAATTTATAATATTTATTAA
948475 AAATACTAATTTATTAAATATTT
1 AAATACTAATTTA-T-AATATTT
948498 TTTCAATAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 35 0.81
27 1 0.02
28 7 0.16
ACGTcount: A:0.47, C:0.04, G:0.01, T:0.48
Consensus pattern (26 bp):
AAATACTAATTTATAATATTTATTAA
Found at i:953252 original size:13 final size:13
Alignment explanation
Indices: 953232--953301 Score: 95
Period size: 13 Copynumber: 5.4 Consensus size: 13
953222 AATAGTCGAT
953232 AATTGATTTGATA
1 AATTGATTTGATA
*
953245 ATTTGATTTGATA
1 AATTGATTTGATA
* *
953258 AATTAATTTGATT
1 AATTGATTTGATA
* *
953271 AGTTGAGTTGATA
1 AATTGATTTGATA
953284 AATTGATTTGATA
1 AATTGATTTGATA
953297 AATTG
1 AATTG
953302 TTTATATAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (13 bp):
AATTGATTTGATA
Found at i:960032 original size:2 final size:2
Alignment explanation
Indices: 960025--960135 Score: 96
Period size: 2 Copynumber: 60.0 Consensus size: 2
960015 TCGGGCCGGG
* * *
960025 TA TA TA TA TA TT TA AA T- TA AA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
960065 TA TA TA TA TA TA TA TA T- TA TA TA TA AA T- TA -A TA TA AA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
960103 TA AA TT TA T- TA -A TA T- 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
960136 ATAATTATTT
Statistics
Matches: 86, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
1 9 0.10
2 77 0.90
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:960078 original size:19 final size:19
Alignment explanation
Indices: 960027--960135 Score: 100
Period size: 19 Copynumber: 5.7 Consensus size: 19
960017 GGGCCGGGTA
* * *
960027 TATATATATTTAAATTAAA
1 TATATATATATATATTATA
960046 TATATATATATATATATATTA
1 TATATATATATATAT-TA-TA
960067 TATATATATATATATTATA
1 TATATATATATATATTATA
* *
960086 TATAAATTAATATAAATTA-A
1 TATATA-T-ATATATATTATA
*
960106 -ATTTAT-TA-ATATTATA
1 TATATATATATATATTATA
960122 TATATATATATATA
1 TATATATATATATA
960136 ATAATTATTT
Statistics
Matches: 73, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
15 5 0.07
16 3 0.04
17 5 0.07
18 3 0.04
19 26 0.36
20 6 0.08
21 25 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATATATATATTATA
Found at i:961997 original size:21 final size:20
Alignment explanation
Indices: 961971--962591 Score: 549
Period size: 21 Copynumber: 29.8 Consensus size: 20
961961 CATATTCATA
961971 TTGCGATAG-TCCAAGTTCGCG
1 TTGCGATAGCTCCAAGTT--CG
*
961992 TTGCGATAG-TCGAAGTTTGCG
1 TTGCGATAGCTCCAAG-TT-CG
* *
962013 TTGCGATCG-TCGAAGTTCGCG
1 TTGCGATAGCTCCAAGTT--CG
* ** *
962034 TTACGAT-TTTCCAAATTCG
1 TTGCGATAGCTCCAAGTTCG
962053 TTGCGATAG-TCCAAGTTTGCG
1 TTGCGATAGCTCCAAG-TT-CG
* *
962074 TTGCGATTTA-TTCCAAATTCG
1 TTGCGA--TAGCTCCAAGTTCG
*
962095 GTGCGATAG-TCCAAGTTCGCG
1 TTGCGATAGCTCCAAGTT--CG
* * * *
962116 TTACGATTTA-TTACAAATTCG
1 TTGCGA--TAGCTCCAAGTTCG
962137 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962158 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962179 TTGCGGTAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962200 TTGCGGTAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962221 TTGCGGTAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
962242 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962263 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
* *
962284 TTGCGGTAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
* *
962305 TTGCGGTAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962326 TTGCGGTAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962347 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962368 TTGCGGTAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962389 TTGCGGTAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
* *
962410 TTGCGGTAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
* * *
962431 TTACGGTAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
962452 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
962473 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
962494 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962515 TTGCGATAGTCTCCAAATTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962536 TTGCGGTAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
962557 TTGCGATAGTCTCCAAGTTCG
1 TTGCGATAG-CTCCAAGTTCG
*
962578 TTGCAATAG-TCCAA
1 TTGCGATAGCTCCAA
962592 AATCGCAACG
Statistics
Matches: 542, Mismatches: 41, Indels: 36
0.88 0.07 0.06
Matches are distributed among these distances:
19 29 0.05
20 4 0.01
21 490 0.90
22 4 0.01
23 15 0.03
ACGTcount: A:0.20, C:0.23, G:0.24, T:0.33
Consensus pattern (20 bp):
TTGCGATAGCTCCAAGTTCG
Found at i:962200 original size:63 final size:63
Alignment explanation
Indices: 962133--962588 Score: 750
Period size: 63 Copynumber: 7.2 Consensus size: 63
962123 TTATTACAAA
*
962133 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
* * *
962196 TTCGTTGCGGTAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAGTTCGTTGCGATAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
* *
962259 TTCGTTGCGATAGTCTCCAAATTCGTTGCGGTAGTCTCCAAATTCGTTGCGGTAGTCTCCAAA
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
* *
962322 TTCGTTGCGGTAGTCTCCAAGTTCGTTGCGATAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
* * *
962385 TTCGTTGCGGTAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAATTCGTTACGGTAGTCTCCAAA
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
* * *
962448 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
* * *
962511 TTCGTTGCGATAGTCTCCAAATTCGTTGCGGTAGTCTCCAAGTTCGTTGCGATAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
*
962574 TTCGTTGCAATAGTC
1 TTCGTTGCGATAGTC
962589 CAAAATCGCA
Statistics
Matches: 368, Mismatches: 25, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 368 1.00
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.34
Consensus pattern (63 bp):
TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
Found at i:962588 original size:42 final size:42
Alignment explanation
Indices: 962133--962581 Score: 736
Period size: 42 Copynumber: 10.7 Consensus size: 42
962123 TTATTACAAA
* *
962133 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAA
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
*
962175 TTCGTTGCGGTAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
* *
962217 TTCGTTGCGGTAGTCTCCAAGTTCGTTGCGATAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
* *
962259 TTCGTTGCGATAGTCTCCAAATTCGTTGCGGTAGTCTCCAAA
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
* *
962301 TTCGTTGCGGTAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
*
962343 TTCGTTGCGATAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
* *
962385 TTCGTTGCGGTAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAA
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
* * * *
962427 TTCGTTACGGTAGTCTCCAAATTCGTTGCGATAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
*
962469 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGATAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
*
962511 TTCGTTGCGATAGTCTCCAAATTCGTTGCGGTAGTCTCCAAG
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
962553 TTCGTTGCGATAGTCTCCAAGTTCGTTGC
1 TTCGTTGCGATAGTCTCCAAGTTCGTTGC
962582 AATAGTCCAA
Statistics
Matches: 383, Mismatches: 24, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 383 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (42 bp):
TTCGTTGCGATAGTCTCCAAGTTCGTTGCGGTAGTCTCCAAG
Found at i:963870 original size:15 final size:15
Alignment explanation
Indices: 963848--963885 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
963838 TTCCAGAAAA
963848 TGGTTCTTG-GTTTTG
1 TGGTTCTTGCG-TTTG
*
963863 TTGTTCTTGCGTTTG
1 TGGTTCTTGCGTTTG
963878 TGGTTCTT
1 TGGTTCTT
963886 TCTCGTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.00, C:0.11, G:0.29, T:0.61
Consensus pattern (15 bp):
TGGTTCTTGCGTTTG
Found at i:964573 original size:38 final size:37
Alignment explanation
Indices: 964423--964657 Score: 241
Period size: 38 Copynumber: 6.7 Consensus size: 37
964413 AATACATATA
* *
964423 TTTCAAAAATATTTTTTAAACTATATA-T-TAT-A--
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
* * * *
964455 TTTAAAAAAAGTTTTCAAAAC--TATATTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
*
964489 TTTC-AAAATG-TTTT-AAA--A-ATATTATATAAGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
* *
964520 TTTAAAAAACGTTTTTAAAACTATATATTATATAATT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
964557 TATTCAAAAATGTTTTTAAAACTATATATTATATAATT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAATT
964595 TATTCAAAAATGTTTTTAAAACTATATATTATATAAGTT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAA-TT
*
964634 TTT--AAAATGATTTTAAAACTATAT
1 TTTCAAAAATGTTTTTAAAACTATAT
964658 GTTACCCATA
Statistics
Matches: 175, Mismatches: 14, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
30 13 0.07
31 10 0.06
32 28 0.16
33 9 0.05
34 6 0.03
36 21 0.12
37 13 0.07
38 72 0.41
39 3 0.02
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
Found at i:964677 original size:36 final size:35
Alignment explanation
Indices: 964460--964682 Score: 167
Period size: 38 Copynumber: 6.3 Consensus size: 35
964450 TTATATTTAA
* *
964460 AAAAAGTTTTCAAAACTATAT-T-ATAT-AGTTTTC
1 AAAATGTTTT-AAAACTATATATTACATAAGTTTTC
* *
964493 AAAATGTTTT-AAA--A-ATATTATATAAGTTTTAA
1 AAAATGTTTTAAAACTATATATTACATAAGTTTT-C
* * *
964525 AAAACGTTTTTAAAACTATATATTATATAATTTATTC
1 AAAATG-TTTTAAAACTATATATTACATAAGTT-TTC
* *
964562 AAAAATGTTTTTAAAACTATATATTATATAATTTATTC
1 -AAAATG-TTTTAAAACTATATATTACATAAGTT-TTC
* *
964600 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTT
1 -AAAATG-TTTTAAAACTATATATTACATAAGTTTTC
*
964637 AAAATGATTTTAAAACTATATGTTACCCAT-A-TTTTC
1 AAAATG-TTTTAAAACTATATATTA--CATAAGTTTTC
964673 AAAATGTTTT
1 AAAATGTTTT
964683 CTTTTTAAAA
Statistics
Matches: 165, Mismatches: 12, Indels: 24
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.01
29 2 0.01
30 4 0.02
31 9 0.05
32 5 0.03
33 13 0.08
34 3 0.02
35 4 0.02
36 34 0.21
37 16 0.10
38 73 0.44
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (35 bp):
AAAATGTTTTAAAACTATATATTACATAAGTTTTC
Found at i:965516 original size:84 final size:84
Alignment explanation
Indices: 965400--966025 Score: 848
Period size: 84 Copynumber: 7.5 Consensus size: 84
965390 TCGGGAGTCT
* * * * * *
965400 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
965465 CGAACTCGAAGGTCTTTTG
66 CGAACTCGAAGGTCTTTTG
* ** * * * * * * *
965484 GTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGTGTAA
*
965549 TCGAACT-TAAGGGTC---T-
65 TCGAACTCGAA-GGTCTTTTG
* * * *
965565 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
965630 CGAACTCGAAGGTCTTTTG
66 CGAACTCGAAGGTCTTTTG
*
965649 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
*
965714 CGAACTCAAAGGTCTTTTG
66 CGAACTCGAAGGTCTTTTG
* * * * * *
965733 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGAGTGTAA
*
965798 TCGAACTCGAAGGTCTTTGG
65 TCGAACTCGAAGGTCTTTTG
* *
965818 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
965883 CGAACTCGAAGGTCTTTTG
66 CGAACTCGAAGGTCTTTTG
*
965902 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
*
965967 CGAACTCAAAGGTCTTTTG
66 CGAACTCGAAGGTCTTTTG
* * * *
965986 TTGGCAGACAACCCTTCTAGACTTAAGCTAAGCTGCAAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAAT
966026 AGTTTGTTTA
Statistics
Matches: 471, Mismatches: 63, Indels: 16
0.86 0.11 0.03
Matches are distributed among these distances:
80 25 0.05
81 38 0.08
82 1 0.00
83 1 0.00
84 305 0.65
85 101 0.21
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
CGAACTCGAAGGTCTTTTG
Found at i:965567 original size:165 final size:166
Alignment explanation
Indices: 965355--966025 Score: 798
Period size: 165 Copynumber: 4.0 Consensus size: 166
965345 GCTATGTTGT
* * * ** *
965355 AAATGATATGACCCCGCAGTTGAGTGTAATCGAAC-TCGGGAGTC-T-TTGGCAGATAGCCCTTC
1 AAATGATATG-CCTCGGAGCTGAGTGTAATCGAACTTAAGG-GTCTTGTTGGCAGATAACCCTTC
* * *
965417 TCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
64 TCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTT
** * * *
965482 TGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGT
129 TGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * *
965520 AAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTTAAGGGTC-T-TTGGCAGATAGCCCTTCT
1 AAATGATATG-CCTCGGAGCTGAGTGTAATCGAACTTAAGGGTCTTGTTGGCAGATAACCCTTCT
*
965583 CGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTT
65 CGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTT
* * *
965648 GTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGC
130 GGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * * *
965685 AAATGATATGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTC
1 AAATGATATGCCTCGGAGCTGAGTGTAATCGAACTTAAGGGTC--TTGTTGGCAGATAACCCTTC
* * * * * * *
965750 TAGACTTAAGTTGTGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAAGGTC-T
64 TCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTT
*
965814 TTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGC
128 TTGG-TGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
* * * *
965854 AAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTTGTTGGCAGATAACCCTT
1 AAATGATATGCCTCGGAGCTGAGTGTAATCGAACT-TAAGGGTC--TTGTTGGCAGATAACCCTT
* * * *
965918 CTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTT
63 CTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTT
* * * *
965983 TTGTTGGCAGACAACCCTTCTAGACTTAAGCTAAGCTGC
128 TTGGTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
966022 AAAT
1 AAAT
966026 AGTTTGTTTA
Statistics
Matches: 447, Mismatches: 50, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
164 29 0.06
165 153 0.34
166 3 0.01
167 1 0.00
168 109 0.24
169 150 0.34
170 2 0.00
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (166 bp):
AAATGATATGCCTCGGAGCTGAGTGTAATCGAACTTAAGGGTCTTGTTGGCAGATAACCCTTCTC
GACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAATCGAACTCGAAGGTCTTTTG
GTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGC
Found at i:965827 original size:169 final size:168
Alignment explanation
Indices: 965400--966025 Score: 839
Period size: 169 Copynumber: 3.7 Consensus size: 168
965390 TCGGGAGTCT
* * * *
965400 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAAT
** * * * *
965465 CGAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGT
66 CGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATAT
* * * *
965529 GCCCTCGAAGCTGAGTGTAATCGAACTTAAGGGTC---T-
130 G-CCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTG
* *
965565 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAAT
* * *
965630 CGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATG
66 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG
965695 CCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTG
131 CCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTG
* * * * * * * *
965733 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAA
*
965798 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
65 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATAT
* * *
965863 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
130 GCCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTG
* * *
965902 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAAT
* * * * *
965967 CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGCTAAGCTGCAAAT
66 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAAT
966026 AGTTTGTTTA
Statistics
Matches: 412, Mismatches: 43, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
164 33 0.08
165 114 0.28
167 1 0.00
168 110 0.27
169 154 0.37
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (168 bp):
TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAAT
CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG
CCTTGGAGCTGAGTGTAATCGAACTCAAAGGTCTTTTG
Found at i:965918 original size:253 final size:249
Alignment explanation
Indices: 965400--966025 Score: 1011
Period size: 253 Copynumber: 2.5 Consensus size: 249
965390 TCGGGAGTCT
* * * * * * *
965400 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCATATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
* * ** * * * *
965465 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
66 CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
* *
965530 CCCTCGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTGAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTA
965595 TGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
196 TGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
965649 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
*
965714 CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTG
66 CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
965779 CCCTCGAAGCTGAGTGTAATCGAACTCGAA-GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
131 CCCTCGAAGCTGAGTGTAATCGAACT-GAAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTA
*
965843 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
191 AGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
965902 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
1 TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
* *
965967 CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGCTAAGCTGCAAAT
66 CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAAT
966026 AGTTTGTTTA
Statistics
Matches: 350, Mismatches: 22, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
249 144 0.41
250 2 0.01
251 1 0.00
253 203 0.58
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (249 bp):
TTGGCAGATAACCCTTCTCGATTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAAT
CGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG
CCCTCGAAGCTGAGTGTAATCGAACTGAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTA
TGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTG
Found at i:971276 original size:15 final size:15
Alignment explanation
Indices: 971254--971291 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
971244 TTCCAGAAAA
971254 TGGTTCTTG-GTTTTG
1 TGGTTCTTGCG-TTTG
*
971269 TTGTTCTTGCGTTTG
1 TGGTTCTTGCGTTTG
971284 TGGTTCTT
1 TGGTTCTT
971292 TCTCGTGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 19 0.95
16 1 0.05
ACGTcount: A:0.00, C:0.11, G:0.29, T:0.61
Consensus pattern (15 bp):
TGGTTCTTGCGTTTG
Found at i:971980 original size:38 final size:37
Alignment explanation
Indices: 971830--972064 Score: 241
Period size: 38 Copynumber: 6.7 Consensus size: 37
971820 AATACATATA
* *
971830 TTTCAAAAATATTTTTTAAACTATATA-T-TAT-A--
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
* * * *
971862 TTTAAAAAAAGTTTTCAAAAC--TATATTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
*
971896 TTTC-AAAATG-TTTT-AAA--A-ATATTATATAAGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
* *
971927 TTTAAAAAACGTTTTTAAAACTATATATTATATAATT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
971964 TATTCAAAAATGTTTTTAAAACTATATATTATATAATT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAATT
972002 TATTCAAAAATGTTTTTAAAACTATATATTATATAAGTT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAA-TT
*
972041 TTT--AAAATGATTTTAAAACTATAT
1 TTTCAAAAATGTTTTTAAAACTATAT
972065 GTTACCCATA
Statistics
Matches: 175, Mismatches: 14, Indels: 24
0.82 0.07 0.11
Matches are distributed among these distances:
30 13 0.07
31 10 0.06
32 28 0.16
33 9 0.05
34 6 0.03
36 21 0.12
37 13 0.07
38 72 0.41
39 3 0.02
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (37 bp):
TTTCAAAAATGTTTTTAAAACTATATATTATATAATT
Found at i:972084 original size:36 final size:35
Alignment explanation
Indices: 971867--972089 Score: 167
Period size: 38 Copynumber: 6.3 Consensus size: 35
971857 TTATATTTAA
* *
971867 AAAAAGTTTTCAAAACTATAT-T-ATAT-AGTTTTC
1 AAAATGTTTT-AAAACTATATATTACATAAGTTTTC
* *
971900 AAAATGTTTT-AAA--A-ATATTATATAAGTTTTAA
1 AAAATGTTTTAAAACTATATATTACATAAGTTTT-C
* * *
971932 AAAACGTTTTTAAAACTATATATTATATAATTTATTC
1 AAAATG-TTTTAAAACTATATATTACATAAGTT-TTC
* *
971969 AAAAATGTTTTTAAAACTATATATTATATAATTTATTC
1 -AAAATG-TTTTAAAACTATATATTACATAAGTT-TTC
* *
972007 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTT
1 -AAAATG-TTTTAAAACTATATATTACATAAGTTTTC
*
972044 AAAATGATTTTAAAACTATATGTTACCCAT-A-TTTTC
1 AAAATG-TTTTAAAACTATATATTA--CATAAGTTTTC
972080 AAAATGTTTT
1 AAAATGTTTT
972090 CTTTTTAAAA
Statistics
Matches: 165, Mismatches: 12, Indels: 24
0.82 0.06 0.12
Matches are distributed among these distances:
28 2 0.01
29 2 0.01
30 4 0.02
31 9 0.05
32 5 0.03
33 13 0.08
34 3 0.02
35 4 0.02
36 34 0.21
37 16 0.10
38 73 0.44
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.45
Consensus pattern (35 bp):
AAAATGTTTTAAAACTATATATTACATAAGTTTTC
Found at i:972419 original size:39 final size:38
Alignment explanation
Indices: 972361--972438 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 38
972351 TTCGTCTCGG
*
972361 GTCGGGTCGTAGTCATGGTCGTGGTAATACGTGTCTTC
1 GTCGGGTCGTAGTCATGGTCATGGTAATACGTGTCTTC
* *
972399 GTCGTGGTCGTGGTCGTGGTCATGGTAATACGTGTCTTC
1 GTCG-GGTCGTAGTCATGGTCATGGTAATACGTGTCTTC
972438 G
1 G
972439 ACACGTCCGC
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 4 0.11
39 32 0.89
ACGTcount: A:0.12, C:0.18, G:0.36, T:0.35
Consensus pattern (38 bp):
GTCGGGTCGTAGTCATGGTCATGGTAATACGTGTCTTC
Found at i:972568 original size:29 final size:29
Alignment explanation
Indices: 972526--972582 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
972516 TGGACTATCG
*
972526 CAACGAATTTGGAGACTATCGCAACGAAC
1 CAACGAACTTGGAGACTATCGCAACGAAC
972555 CAACGAACTTGGAGACTATCGCAACGAA
1 CAACGAACTTGGAGACTATCGCAACGAA
972583 TTTGTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.39, C:0.25, G:0.21, T:0.16
Consensus pattern (29 bp):
CAACGAACTTGGAGACTATCGCAACGAAC
Found at i:972617 original size:21 final size:21
Alignment explanation
Indices: 972593--972647 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
972583 TTTGTAATAA
*
972593 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTAGACT
* *
972614 ATCGCAACACAAACTTAGACT
1 ATCGCAACGCGAACTTAGACT
*
972635 ATCGCAATGCGAA
1 ATCGCAACGCGAA
972648 TATGTAAATC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.36, C:0.29, G:0.16, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCGAACTTAGACT
Found at i:988193 original size:16 final size:16
Alignment explanation
Indices: 988154--988202 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 16
988144 GTATCTTCTA
988154 TTTTCTGTTTATCATC
1 TTTTCTGTTTATCATC
* *
988170 --TTC-ATTTATTATC
1 TTTTCTGTTTATCATC
988183 TTTTCTGTTTATCAT-
1 TTTTCTGTTTATCATC
988198 TTTTC
1 TTTTC
988203 ATTTGAACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 8 0.31
14 3 0.12
15 8 0.31
16 7 0.27
ACGTcount: A:0.14, C:0.16, G:0.04, T:0.65
Consensus pattern (16 bp):
TTTTCTGTTTATCATC
Found at i:988194 original size:13 final size:14
Alignment explanation
Indices: 988153--988200 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
988143 GGTATCTTCT
988153 ATTTTCTGTTTATC
1 ATTTTCTGTTTATC
* *
988167 ATCTTCATTTATTATC
1 ATTTTC-TGT-TTATC
988183 -TTTTCTGTTTATC
1 ATTTTCTGTTTATC
988196 ATTTT
1 ATTTT
988201 TCATTTGAAC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
13 5 0.19
14 11 0.41
15 6 0.22
16 5 0.19
ACGTcount: A:0.17, C:0.15, G:0.04, T:0.65
Consensus pattern (14 bp):
ATTTTCTGTTTATC
Found at i:991431 original size:8 final size:8
Alignment explanation
Indices: 991119--991420 Score: 352
Period size: 8 Copynumber: 38.9 Consensus size: 8
991109 TATAATTTTA
991119 CATACATG
1 CATACATG
991127 CATACATG
1 CATACATG
991135 CATACATG
1 CATACATG
991143 CATACATG
1 CATACATG
991151 CATACAT-
1 CATACATG
991158 C---CAT-
1 CATACATG
*
991162 CATACATA
1 CATACATG
991170 CATACATG
1 CATACATG
991178 CATACATG
1 CATACATG
991186 CATACATG
1 CATACATG
991194 CATACATG
1 CATACATG
991202 CATACATG
1 CATACATG
991210 CATACATG
1 CATACATG
*
991218 CATCCATG
1 CATACATG
*
991226 CATACATC
1 CATACATG
*
991234 CATCCATG
1 CATACATG
*
991242 CATCCATG
1 CATACATG
*
991250 CATCCATG
1 CATACATG
*
991258 CATCCATG
1 CATACATG
* *
991266 CATGCATC
1 CATACATG
* *
991274 CATGCATC
1 CATACATG
* *
991282 CATGCATC
1 CATACATG
*
991290 CATCCATG
1 CATACATG
*
991298 CATCCATG
1 CATACATG
*
991306 CATCCATG
1 CATACATG
* *
991314 CATGCATC
1 CATACATG
*
991322 CATGCATG
1 CATACATG
991330 CATACATG
1 CATACATG
*
991338 CATCCATG
1 CATACATG
991346 CATACATG
1 CATACATG
*
991354 CATCCATG
1 CATACATG
991362 CATACATG
1 CATACATG
991370 ----CATG
1 CATACATG
991374 CATACATG
1 CATACATG
991382 CATACATG
1 CATACATG
991390 CATACATG
1 CATACATG
991398 CATACATG
1 CATACATG
991406 CATACATG
1 CATACATG
991414 CATACAT
1 CATACAT
991421 ACATGCATAC
Statistics
Matches: 268, Mismatches: 18, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
4 8 0.03
7 4 0.01
8 256 0.96
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (8 bp):
CATACATG
Found at i:999438 original size:5 final size:5
Alignment explanation
Indices: 999428--999473 Score: 92
Period size: 5 Copynumber: 9.2 Consensus size: 5
999418 AGTTGTTTAG
999428 CCACT CCACT CCACT CCACT CCACT CCACT CCACT CCACT CCACT C
1 CCACT CCACT CCACT CCACT CCACT CCACT CCACT CCACT CCACT C
999474 TTCACTTCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.20, C:0.61, G:0.00, T:0.20
Consensus pattern (5 bp):
CCACT
Found at i:1019978 original size:2 final size:2
Alignment explanation
Indices: 1019971--1019996 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1019961 CTCACTTTGA
1019971 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
1019997 TAATCTCAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1027335 original size:20 final size:21
Alignment explanation
Indices: 1027310--1027349 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1027300 AATGTTATCT
*
1027310 AAAATATT-ATTTTTTTACCG
1 AAAATATTAATTTTGTTACCG
1027330 AAAATATTAATTTTGTTACC
1 AAAATATTAATTTTGTTACC
1027350 TAATTTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (21 bp):
AAAATATTAATTTTGTTACCG
Found at i:1028094 original size:49 final size:49
Alignment explanation
Indices: 1028004--1028110 Score: 124
Period size: 49 Copynumber: 2.2 Consensus size: 49
1027994 CAACATGAAT
*
1028004 ATCTCAATATTGTGAGAGTAGAGCATCTCGACTCTACTCAAGCAGAAGC
1 ATCTCAATATTGTGAGAGTAGAACATCTCGACTCTACTCAAGCAGAAGC
* * * * ** * *
1028053 ATCTCAATCTTGTGAGAGTGGAATATCTCGATTCTGTTCAAGCTGAGGC
1 ATCTCAATATTGTGAGAGTAGAACATCTCGACTCTACTCAAGCAGAAGC
*
1028102 TTCTCAATA
1 ATCTCAATA
1028111 GGGACATCTC
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (49 bp):
ATCTCAATATTGTGAGAGTAGAACATCTCGACTCTACTCAAGCAGAAGC
Found at i:1028899 original size:21 final size:19
Alignment explanation
Indices: 1028874--1028934 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 19
1028864 GAACTTCGAC
1028874 TATCGCAACGAATTTGGAA
1 TATCGCAACGAATTTGGAA
* * *
1028893 TAAATCGCAACGCGAACTTCGAC
1 T--ATCGCAA--CGAATTTGGAA
1028916 TATCGCAACGAATTTGGAA
1 TATCGCAACGAATTTGGAA
1028935 ACTGATTTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
19 9 0.28
21 14 0.44
23 9 0.28
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (19 bp):
TATCGCAACGAATTTGGAA
Found at i:1030398 original size:19 final size:19
Alignment explanation
Indices: 1030374--1030419 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1030364 GTTTCTCCGA
*
1030374 AAATTTAGT-GGTCTCCTCT
1 AAATTTAGTAGTTC-CCTCT
1030393 AAATTTTAGTAGTTCCCTCT
1 AAA-TTTAGTAGTTCCCTCT
1030413 AAATTTA
1 AAATTTA
1030420 AGTTTGTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.43
Consensus pattern (19 bp):
AAATTTAGTAGTTCCCTCT
Found at i:1035051 original size:37 final size:37
Alignment explanation
Indices: 1035010--1035082 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
1035000 ATGTTGCTCT
* * *
1035010 TGTGTAATGTACTAATAAATGATGGTTAGAAAAGTAG
1 TGTGTAATATACTAATAAAAGATGGTAAGAAAAGTAG
1035047 TGTGTAATATACTAATAAAAGATGGTAAGAAAAGTA
1 TGTGTAATATACTAATAAAAGATGGTAAGAAAAGTA
1035083 TCCTAGTAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.30
Consensus pattern (37 bp):
TGTGTAATATACTAATAAAAGATGGTAAGAAAAGTAG
Found at i:1040225 original size:31 final size:30
Alignment explanation
Indices: 1040187--1040245 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 30
1040177 CCTTATTCGC
*
1040187 GCCTTCCATCTACCTGTTAGAAAGAGTGCAT
1 GCCTTCCATCTACCTGTCAGAAA-AGTGCAT
1040218 GCCTTCCATCTACCTGTCAGAAAAGTGC
1 GCCTTCCATCTACCTGTCAGAAAAGTGC
1040246 TAGATCGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 5 0.19
31 22 0.81
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (30 bp):
GCCTTCCATCTACCTGTCAGAAAAGTGCAT
Found at i:1040691 original size:21 final size:19
Alignment explanation
Indices: 1040632--1040699 Score: 100
Period size: 19 Copynumber: 3.5 Consensus size: 19
1040622 TCTACAGTTG
*
1040632 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTACAAAT
*
1040651 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTACAAAT
1040670 TCGTTGCGATAGTTTACAAAT
1 TCGTTGCGAT--TTTACAAAT
1040691 TCGTTGCGA
1 TCGTTGCGA
1040700 AAATTCGTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 28 0.62
21 17 0.38
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.41
Consensus pattern (19 bp):
TCGTTGCGATTTTACAAAT
Found at i:1041344 original size:6 final size:6
Alignment explanation
Indices: 1041319--1041354 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
1041309 TCTCGTCTCG
1041319 GGTCG- GGTCG- GGTC-T GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1041355 AATACGTGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 13 0.45
6 16 0.55
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:1041535 original size:43 final size:41
Alignment explanation
Indices: 1041450--1041557 Score: 135
Period size: 43 Copynumber: 2.6 Consensus size: 41
1041440 ACGAATTTTT
*
1041450 GCAACGAATTTGGAAAATCGCAACGACAAATGTACACCATC
1 GCAACGAATTTGGAAAATCGCAACAACAAATGTACACCATC
** * * *
1041491 GCAACGAATTTGTAGACTATCGCAACAACAACTGTAGACTATC
1 GCAACGAATTTG--GAAAATCGCAACAACAAATGTACACCATC
*
1041534 GCAACGAATCTGGAAAATCGCAAC
1 GCAACGAATTTGGAAAATCGCAAC
1041558 GAATTTAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
41 22 0.39
43 34 0.61
ACGTcount: A:0.40, C:0.24, G:0.18, T:0.19
Consensus pattern (41 bp):
GCAACGAATTTGGAAAATCGCAACAACAAATGTACACCATC
Found at i:1041553 original size:19 final size:19
Alignment explanation
Indices: 1041531--1041578 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
1041521 ACTGTAGACT
**
1041531 ATCGCAACGAATCTGGAAA
1 ATCGCAACGAATCTAAAAA
*
1041550 ATCGCAACGAATTTAAAAA
1 ATCGCAACGAATCTAAAAA
1041569 ATCGCAACGA
1 ATCGCAACGA
1041579 CAACTGTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.46, C:0.21, G:0.17, T:0.17
Consensus pattern (19 bp):
ATCGCAACGAATCTAAAAA
Found at i:1041594 original size:22 final size:21
Alignment explanation
Indices: 1041466--1041599 Score: 96
Period size: 22 Copynumber: 6.4 Consensus size: 21
1041456 AATTTGGAAA
* * *
1041466 ATCGCAACGACAAATGTACACC
1 ATCGCAACGA-AACTGTAAACT
** *
1041488 ATCGCAACGAATTTGTAGACT
1 ATCGCAACGAAACTGTAAACT
* *
1041509 ATCGCAACAACAACTGTAGACT
1 ATCGCAACGA-AACTGTAAACT
* *
1041531 ATCGCAACGAATCTGGAAA--
1 ATCGCAACGAAACTGTAAACT
* **
1041550 ATCGCAACG-AA-TTTAAAAA
1 ATCGCAACGAAACTGTAAACT
1041569 ATCGCAACGACAACTGTAAACT
1 ATCGCAACGA-AACTGTAAACT
1041591 ATCGCAACG
1 ATCGCAACG
1041600 CGAAATAGAG
Statistics
Matches: 89, Mismatches: 17, Indels: 12
0.75 0.14 0.10
Matches are distributed among these distances:
17 4 0.04
18 1 0.01
19 18 0.20
21 24 0.27
22 42 0.47
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAAACTGTAAACT
Found at i:1044431 original size:23 final size:21
Alignment explanation
Indices: 1044404--1044453 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 21
1044394 TATCGAATAC
1044404 AAAAATTAATTAAACAAAAATAAT
1 AAAAA-TAATT-AA-AAAAATAAT
*
1044428 AAAAATAATTAATAAAATAAT
1 AAAAATAATTAAAAAAATAAT
1044449 AAAAA
1 AAAAA
1044454 ATAGGAAGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 13 0.52
22 2 0.08
23 5 0.20
24 5 0.20
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAATAATTAAAAAAATAAT
Found at i:1046416 original size:19 final size:19
Alignment explanation
Indices: 1046389--1046427 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1046379 AAATGACCAA
1046389 CAAAATCGCAATGCGATCT
1 CAAAATCGCAATGCGATCT
* *
1046408 CAAATTCGCATTGCGATCT
1 CAAAATCGCAATGCGATCT
1046427 C
1 C
1046428 CACTATCGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (19 bp):
CAAAATCGCAATGCGATCT
Found at i:1046626 original size:6 final size:6
Alignment explanation
Indices: 1046615--1046645 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1046605 GGCACGTATT
1046615 ACCACG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
1046646 GACGAGACGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.35, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1047479 original size:104 final size:104
Alignment explanation
Indices: 1047299--1047507 Score: 400
Period size: 104 Copynumber: 2.0 Consensus size: 104
1047289 AATTTTCGAC
1047299 GTTGTATCATTTATACAATTGAAATTTCAATTCTGCCAATTATAGCACCGAACATTGATTTTCAT
1 GTTGTATCATTTATACAATTGAAATTTCAATTCTGCCAATTATAGCACCGAACATTGATTTTCAT
*
1047364 TTCAATTTTACCACTAGGTCGTTAAATCGTTAACAACAA
66 TTCAATTTTACCACTAGGTCGTTAAATCATTAACAACAA
*
1047403 GTTGTATCATTTATACGATTGAAATTTCAATTCTGCCAATTATAGCACCGAACATTGATTTTCAT
1 GTTGTATCATTTATACAATTGAAATTTCAATTCTGCCAATTATAGCACCGAACATTGATTTTCAT
1047468 TTCAATTTTACCACTAGGTCGTTAAATCATTAACAACAA
66 TTCAATTTTACCACTAGGTCGTTAAATCATTAACAACAA
1047507 G
1 G
1047508 ATCAAAACGA
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.33, C:0.18, G:0.11, T:0.37
Consensus pattern (104 bp):
GTTGTATCATTTATACAATTGAAATTTCAATTCTGCCAATTATAGCACCGAACATTGATTTTCAT
TTCAATTTTACCACTAGGTCGTTAAATCATTAACAACAA
Found at i:1056508 original size:23 final size:23
Alignment explanation
Indices: 1056482--1056536 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
1056472 ACTTAACATA
1056482 AAAAATA-AAGAAAAACGTGTCAT
1 AAAAATATAAG-AAAACGTGTCAT
* * *
1056505 AAAATTATAAGAATACGTGTTAT
1 AAAAATATAAGAAAACGTGTCAT
*
1056528 AAAGATATA
1 AAAAATATA
1056537 TTTATAAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.56, C:0.05, G:0.13, T:0.25
Consensus pattern (23 bp):
AAAAATATAAGAAAACGTGTCAT
Found at i:1067682 original size:37 final size:37
Alignment explanation
Indices: 1067632--1067743 Score: 197
Period size: 37 Copynumber: 3.0 Consensus size: 37
1067622 TGAAAGAAAC
* *
1067632 GTATGATAAGATTTCTCTACGATGTTATAGGTTGAAT
1 GTATGATAAGATTTCTCTACGATGTTATGGGTAGAAT
*
1067669 GTATGATAAGATTTCTCTATGATGTTATGGGTAGAAT
1 GTATGATAAGATTTCTCTACGATGTTATGGGTAGAAT
1067706 GTATGATAAGATTTCTCTACGATGTTATGGGTAGAAT
1 GTATGATAAGATTTCTCTACGATGTTATGGGTAGAAT
1067743 G
1 G
1067744 AGTTCTGTTT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 71 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.39
Consensus pattern (37 bp):
GTATGATAAGATTTCTCTACGATGTTATGGGTAGAAT
Found at i:1083622 original size:16 final size:16
Alignment explanation
Indices: 1083601--1083639 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1083591 TTTCTAAAAG
*
1083601 CTAAAAGCTTTTGCAA
1 CTAAAAGCTATTGCAA
1083617 CTAAAAGCTATTGCAA
1 CTAAAAGCTATTGCAA
*
1083633 CAAAAAG
1 CTAAAAG
1083640 AACTTATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (16 bp):
CTAAAAGCTATTGCAA
Found at i:1083734 original size:16 final size:16
Alignment explanation
Indices: 1083713--1083751 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
1083703 TTTCTAAAAG
*
1083713 CTAAAAGCTTTTGCAA
1 CTAAAAGCTATTGCAA
1083729 CTAAAAGCTATTGCAA
1 CTAAAAGCTATTGCAA
*
1083745 CAAAAAG
1 CTAAAAG
1083752 AACTTATCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (16 bp):
CTAAAAGCTATTGCAA
Found at i:1083801 original size:113 final size:112
Alignment explanation
Indices: 1083536--1083811 Score: 543
Period size: 112 Copynumber: 2.5 Consensus size: 112
1083526 CAGTAAAATC
1083536 ATAGGACGTAAAAACAGTTCATTCATTTAAGCAACAAAAAAACAACTTGTTTATGTTTCTAAAAG
1 ATAGGACGTAAAAACAGTTCATTCATTTAAGCAAC-AAAAAACAACTTGTTTATGTTTCTAAAAG
1083601 CTAAAAGCTTTTGCAACTAAAAGCTATTGCAACAAAAAGAACTTATCT
65 CTAAAAGCTTTTGCAACTAAAAGCTATTGCAACAAAAAGAACTTATCT
1083649 ATAGGACGTAAAAACAGTTCATTCATTTAAGCAACAAAAAACAACTTGTTTATGTTTCTAAAAGC
1 ATAGGACGTAAAAACAGTTCATTCATTTAAGCAACAAAAAACAACTTGTTTATGTTTCTAAAAGC
1083714 TAAAAGCTTTTGCAACTAAAAGCTATTGCAACAAAAAGAACTTATCT
66 TAAAAGCTTTTGCAACTAAAAGCTATTGCAACAAAAAGAACTTATCT
1083761 ATAGGACGTAAAAACAGTTCATTCATTTAAGCAACAAAAAACAACTTGTTT
1 ATAGGACGTAAAAACAGTTCATTCATTTAAGCAACAAAAAACAACTTGTTT
1083812 TAGTACACAT
Statistics
Matches: 163, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
112 128 0.79
113 35 0.21
ACGTcount: A:0.44, C:0.16, G:0.12, T:0.28
Consensus pattern (112 bp):
ATAGGACGTAAAAACAGTTCATTCATTTAAGCAACAAAAAACAACTTGTTTATGTTTCTAAAAGC
TAAAAGCTTTTGCAACTAAAAGCTATTGCAACAAAAAGAACTTATCT
Found at i:1088571 original size:47 final size:47
Alignment explanation
Indices: 1088502--1088596 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
1088492 AAAATCTAAC
1088502 TTAGTTCCATGCAAACCTGAAGCCTCCTTCCGTAATTTCTCTTGGTA
1 TTAGTTCCATGCAAACCTGAAGCCTCCTTCCGTAATTTCTCTTGGTA
1088549 TTAGTTCCATGCAAACCTGAAGCCTCCTTCCGTAATTTCTCTTGGTA
1 TTAGTTCCATGCAAACCTGAAGCCTCCTTCCGTAATTTCTCTTGGTA
1088596 T
1 T
1088597 AATTTTTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.21, C:0.27, G:0.15, T:0.37
Consensus pattern (47 bp):
TTAGTTCCATGCAAACCTGAAGCCTCCTTCCGTAATTTCTCTTGGTA
Found at i:1095335 original size:22 final size:23
Alignment explanation
Indices: 1095310--1095353 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1095300 CTTAAAATGT
**
1095310 TAGTTTTT-GTTTGTTTTTATGG
1 TAGTTTTTCGTTTACTTTTATGG
1095332 TAGTTTTTCGTTTACTTTTATG
1 TAGTTTTTCGTTTACTTTTATG
1095354 TTACAGTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.11, C:0.05, G:0.18, T:0.66
Consensus pattern (23 bp):
TAGTTTTTCGTTTACTTTTATGG
Found at i:1098193 original size:2 final size:2
Alignment explanation
Indices: 1098186--1098245 Score: 113
Period size: 2 Copynumber: 30.5 Consensus size: 2
1098176 AAAATTAAGT
1098186 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
1098228 TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA T
1098246 TGATTTTTTA
Statistics
Matches: 57, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 56 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1121618 original size:20 final size:21
Alignment explanation
Indices: 1121585--1121628 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1121575 GATTTAAGGG
*
1121585 TAAATTATGCG-TTTAGTATT
1 TAAATTATGCGTTTTAGTACT
1121605 TAAATTAT-CAGTTTTAGTACT
1 TAAATTATGC-GTTTTAGTACT
1121626 TAA
1 TAA
1121629 TTTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 9 0.43
21 11 0.52
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (21 bp):
TAAATTATGCGTTTTAGTACT
Found at i:1124513 original size:31 final size:31
Alignment explanation
Indices: 1124478--1124540 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
1124468 TTTTAAAAAG
1124478 ATTAA-AAGTTTAAATATTAAAA-TAGACCAAA
1 ATTAATAA-TTTAAATATTAAAATTA-ACCAAA
**
1124509 ATTAATAATTTAGGTATTAAAATTAACCAAA
1 ATTAATAATTTAAATATTAAAATTAACCAAA
1124540 A
1 A
1124541 CAACCTCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (31 bp):
ATTAATAATTTAAATATTAAAATTAACCAAA
Found at i:1134977 original size:149 final size:150
Alignment explanation
Indices: 1134788--1135103 Score: 573
Period size: 150 Copynumber: 2.1 Consensus size: 150
1134778 GGGTAGAGGG
* *
1134788 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTT-GAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
*
1134852 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1134917 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
*
1134937 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
1135002 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
1135067 ATATGGCACTACGGTGCAAT
131 ATATGGCACTACGGTGCAAT
1135087 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1135104 TGCATTTATA
Statistics
Matches: 161, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
149 52 0.32
150 109 0.68
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (150 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTGTGAAGTCTTGGAAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATTATATGTGGTCCTTATGGACATCATT
ATATGGCACTACGGTGCAAT
Found at i:1135115 original size:23 final size:23
Alignment explanation
Indices: 1135071--1135115 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1135061 ATCATTATAT
*
1135071 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
* *
1135094 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
1135116 AGCTGTGGTG
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:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1136568 original size:29 final size:29
Alignment explanation
Indices: 1136463--1136568 Score: 122
Period size: 29 Copynumber: 3.7 Consensus size: 29
1136453 ATTTTTAAAA
* * ***
1136463 TATTTACCAAAATAGCACCCATTTCGAAT
1 TATTTACCAGAATAGCACCAAAACCGAAT
* * *
1136492 TAATTACCAGAATAGCACAAAAACTGAAT
1 TATTTACCAGAATAGCACCAAAACCGAAT
*
1136521 TATTTACCAGAATATCACCAAAACCGAAT
1 TATTTACCAGAATAGCACCAAAACCGAAT
*
1136550 TATTTACTAGAATAGCACC
1 TATTTACCAGAATAGCACC
1136569 GATCAACGGT
Statistics
Matches: 63, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.43, C:0.22, G:0.08, T:0.26
Consensus pattern (29 bp):
TATTTACCAGAATAGCACCAAAACCGAAT
Found at i:1136608 original size:18 final size:18
Alignment explanation
Indices: 1136576--1136628 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
1136566 ACCGATCAAC
*
1136576 GGTCAAC-GATCGGGTCG
1 GGTCAACGGGTCGGGTCG
1136593 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
*
1136611 GGTAAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
1136629 TGACCGGTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
17 7 0.21
18 26 0.79
ACGTcount: A:0.15, C:0.21, G:0.47, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1143878 original size:29 final size:29
Alignment explanation
Indices: 1143843--1143910 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
1143833 CATTTTACAC
* *
1143843 AAATAGCACCCTTTTTAAAATATTTACCA
1 AAATAGCACCCATTTTAAAATAATTACCA
* *
1143872 AAATAGCACCCATTTTGAATTAATTACCA
1 AAATAGCACCCATTTTAAAATAATTACCA
*
1143901 GAATAGCACC
1 AAATAGCACC
1143911 AAAACCGAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.41, C:0.22, G:0.07, T:0.29
Consensus pattern (29 bp):
AAATAGCACCCATTTTAAAATAATTACCA
Found at i:1143920 original size:29 final size:29
Alignment explanation
Indices: 1143888--1143968 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
1143878 CACCCATTTT
*
1143888 GAATTAATTACCAGAATAGCACCAAAACC
1 GAATTATTTACCAGAATAGCACCAAAACC
1143917 GAATTATTTACCAGAATAGCACCAAAACC
1 GAATTATTTACCAGAATAGCACCAAAACC
*
1143946 GAATTATTTACTAGAATAGCACC
1 GAATTATTTACCAGAATAGCACC
1143969 GGTCAACGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (29 bp):
GAATTATTTACCAGAATAGCACCAAAACC
Found at i:1144008 original size:18 final size:17
Alignment explanation
Indices: 1143976--1144014 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 17
1143966 ACCGGTCAAC
1143976 GGTCAACGATCGGGTCG
1 GGTCAACGATCGGGTCG
*
1143993 GGTCAACGGGTCGGGTCG
1 GGTCAAC-GATCGGGTCG
1144011 GGTC
1 GGTC
1144015 GTGACCGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.13, C:0.23, G:0.46, T:0.18
Consensus pattern (17 bp):
GGTCAACGATCGGGTCG
Found at i:1149628 original size:14 final size:15
Alignment explanation
Indices: 1149609--1149637 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1149599 TTTTAAAATC
1149609 TCAAAT-TTTATTTA
1 TCAAATATTTATTTA
1149623 TCAAATATTTATTTA
1 TCAAATATTTATTTA
1149638 GGATACATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (15 bp):
TCAAATATTTATTTA
Found at i:1150403 original size:2 final size:2
Alignment explanation
Indices: 1150396--1150421 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1150386 TATATTATTA
1150396 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
1150422 TCATCGTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1161658 original size:31 final size:31
Alignment explanation
Indices: 1161620--1161678 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1161610 CGAGGGTTAC
*
1161620 CTATGTTCTAT-GGAACATATGGACAGTTTAT
1 CTATGTTCT-TCGAAACATATGGACAGTTTAT
1161651 CTATGTTCTTCGAAACATATGGACAGTT
1 CTATGTTCTTCGAAACATATGGACAGTT
1161679 ACATATGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.29, C:0.15, G:0.19, T:0.37
Consensus pattern (31 bp):
CTATGTTCTTCGAAACATATGGACAGTTTAT
Found at i:1169723 original size:69 final size:70
Alignment explanation
Indices: 1169606--1169741 Score: 220
Period size: 69 Copynumber: 2.0 Consensus size: 70
1169596 TACACTTTCA
* * *
1169606 TTTAAGATATCTTCCTTTTTGAGCAAACACTGATTCCTTAAGGATCTGTCATTCCAAAATGCACC
1 TTTAAGATATCGTCCTTTTTAAGCAAACACTGATCCCTTAAGGATCTGTCATTCCAAAATGCACC
1169671 TCTAT
66 TCTAT
* *
1169676 TTTATGATATCGTCCTTTTTAAGC-ACCACTGATCCCTTAAGGATCTGTCATTCCAAAATGCACC
1 TTTAAGATATCGTCCTTTTTAAGCAAACACTGATCCCTTAAGGATCTGTCATTCCAAAATGCACC
1169740 TC
66 TC
1169742 CCTTTATTCA
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
69 40 0.66
70 21 0.34
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.36
Consensus pattern (70 bp):
TTTAAGATATCGTCCTTTTTAAGCAAACACTGATCCCTTAAGGATCTGTCATTCCAAAATGCACC
TCTAT
Found at i:1171949 original size:21 final size:20
Alignment explanation
Indices: 1171922--1171967 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
1171912 TTCTATTTTG
1171922 CTAAATTTCTA-ATAATTAACC
1 CTAAATTT-TAGA-AATTAACC
*
1171943 TTAAATTTTAGAAATTAACC
1 CTAAATTTTAGAAATTAACC
1171963 CTAAA
1 CTAAA
1171968 CTCACAATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (20 bp):
CTAAATTTTAGAAATTAACC
Found at i:1174326 original size:23 final size:24
Alignment explanation
Indices: 1174300--1174347 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1174290 TATTGACACC
1174300 TTTTATAAAT-TTA-TATTTAAAAA
1 TTTTA-AAATATTATTATTTAAAAA
*
1174323 TTTTAAATTATTATTATTTAAAAA
1 TTTTAAAATATTATTATTTAAAAA
1174347 T
1 T
1174348 CCAAAATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 8 0.36
24 11 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTAAAATATTATTATTTAAAAA
Found at i:1174357 original size:23 final size:23
Alignment explanation
Indices: 1174306--1174357 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
1174296 CACCTTTTAT
**
1174306 AAAT-TTATATTTAAAAATTTTA
1 AAATATTATATTTAAAAATTCCA
*
1174328 AATTATTATTATTTAAAAA-TCCA
1 AAATATTA-TATTTAAAAATTCCA
1174351 AAATATT
1 AAATATT
1174358 TTTAAATTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
22 3 0.12
23 11 0.46
24 10 0.42
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATTATATTTAAAAATTCCA
Found at i:1174666 original size:19 final size:19
Alignment explanation
Indices: 1174642--1174709 Score: 91
Period size: 19 Copynumber: 3.5 Consensus size: 19
1174632 GAAGAATAGG
1174642 AAAAGTTAAGATTTTTTTT
1 AAAAGTTAAGATTTTTTTT
1174661 AAAAGTTAAGATTTTTTTT
1 AAAAGTTAAGATTTTTTTT
* *
1174680 AAAAATTTATGATTTTTTTTT
1 -AAAAGTTAAGA-TTTTTTTT
*
1174701 AAAAATTAA
1 AAAAGTTAA
1174710 AGGAAATAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
19 19 0.44
20 16 0.37
21 8 0.19
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (19 bp):
AAAAGTTAAGATTTTTTTT
Found at i:1174678 original size:20 final size:20
Alignment explanation
Indices: 1174642--1174709 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
1174632 GAAGAATAGG
1174642 AAAAGTTAAGA-TTTTTTTT
1 AAAAGTTAAGATTTTTTTTT
*
1174661 AAAAGTTAAGATTTTTTTTA
1 AAAAGTTAAGATTTTTTTTT
* *
1174681 AAAATTTATGATTTTTTTTT
1 AAAAGTTAAGATTTTTTTTT
*
1174701 AAAAATTAA
1 AAAAGTTAA
1174710 AGGAAATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 11 0.26
20 31 0.74
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (20 bp):
AAAAGTTAAGATTTTTTTTT
Found at i:1176238 original size:53 final size:53
Alignment explanation
Indices: 1176158--1176317 Score: 302
Period size: 53 Copynumber: 3.0 Consensus size: 53
1176148 CTGTTTCACA
**
1176158 GGTCCCTGATATCTAACATTTCGATCATGTAATTATTCATGCATACATCCAGG
1 GGTCCCTGATATCTAACATTTTAATCATGTAATTATTCATGCATACATCCAGG
1176211 GGTCCCTGATATCTAACATTTTAATCATGTAATTATTCATGCATACATCCAGG
1 GGTCCCTGATATCTAACATTTTAATCATGTAATTATTCATGCATACATCCAGG
1176264 GGTCCCTGATATCTAACATTTTAATCATGTAATTATTCATGCATACATCCAGG
1 GGTCCCTGATATCTAACATTTTAATCATGTAATTATTCATGCATACATCCAGG
1176317 G
1 G
1176318 ATGGTCTAGG
Statistics
Matches: 105, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 105 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.35
Consensus pattern (53 bp):
GGTCCCTGATATCTAACATTTTAATCATGTAATTATTCATGCATACATCCAGG
Found at i:1186772 original size:33 final size:33
Alignment explanation
Indices: 1186731--1186835 Score: 194
Period size: 33 Copynumber: 3.2 Consensus size: 33
1186721 AATAAACGTT
1186731 AGCA-TCTTCGGATTCGATGTTGTTGGAGTTAG
1 AGCATTCTTCGGATTCGATGTTGTTGGAGTTAG
*
1186763 AGCATTCTTCGGATTTGATGTTGTTGGAGTTAG
1 AGCATTCTTCGGATTCGATGTTGTTGGAGTTAG
1186796 AGCATTCTTCGGATTCGATGTTGTTGGAGTTAG
1 AGCATTCTTCGGATTCGATGTTGTTGGAGTTAG
1186829 AGCATTC
1 AGCATTC
1186836 ATGTTCATCA
Statistics
Matches: 70, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 4 0.06
33 66 0.94
ACGTcount: A:0.19, C:0.12, G:0.30, T:0.39
Consensus pattern (33 bp):
AGCATTCTTCGGATTCGATGTTGTTGGAGTTAG
Found at i:1189706 original size:2 final size:2
Alignment explanation
Indices: 1189699--1189750 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
1189689 AAGAAGAATG
1189699 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
1189741 AT AT AT AT AT
1 AT AT AT AT AT
1189751 CAACCAGGAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1189878 original size:86 final size:87
Alignment explanation
Indices: 1189730--1189903 Score: 323
Period size: 86 Copynumber: 2.0 Consensus size: 87
1189720 TATATATATA
*
1189730 TATATATATATATATATATATCAACCAGGAGAGAAGGGGAAGAGAAAGCTCACCTACTACAATGA
1 TATATATATATATATATATATCAACCAGGAGAGAAGGGGAAGAGAAAGCTCACCTACAACAATGA
1189795 TAAAAGAGAAGTTTCTTCTTCT
66 TAAAAGAGAAGTTTCTTCTTCT
*
1189817 TATATATATATATATATATATCAACCAGTAG-GAAGGGGAAGAGAAAGCTCACCTACAACAATGA
1 TATATATATATATATATATATCAACCAGGAGAGAAGGGGAAGAGAAAGCTCACCTACAACAATGA
1189881 TAAAAGAGAAGTTTCTTCTTCT
66 TAAAAGAGAAGTTTCTTCTTCT
1189903 T
1 T
1189904 CTTCTTCTTC
Statistics
Matches: 85, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
86 55 0.65
87 30 0.35
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (87 bp):
TATATATATATATATATATATCAACCAGGAGAGAAGGGGAAGAGAAAGCTCACCTACAACAATGA
TAAAAGAGAAGTTTCTTCTTCT
Found at i:1190643 original size:7 final size:7
Alignment explanation
Indices: 1190631--1190658 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
1190621 CATATCTTAT
1190631 TTTCGAC
1 TTTCGAC
1190638 TTTCGAC
1 TTTCGAC
1190645 TTTCGAC
1 TTTCGAC
1190652 TTTCGAC
1 TTTCGAC
1190659 GTAATTGGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (7 bp):
TTTCGAC
Found at i:1191967 original size:20 final size:19
Alignment explanation
Indices: 1191923--1191970 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
1191913 ATATAATTTT
1191923 AATTTTTTAATTTTAAATA
1 AATTTTTTAATTTTAAATA
1191942 AATTTTTTAATTTTAAATA
1 AATTTTTTAATTTTAAATA
1191961 AATTTTTTAA
1 AATTTTTTAA
1191971 AATTACCTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
AATTTTTTAATTTTAAATA
Found at i:1194492 original size:20 final size:20
Alignment explanation
Indices: 1194469--1194518 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
1194459 CTTTTGCAGA
1194469 AGTATCGATACTCTTGGGCT
1 AGTATCGATACTCTTGGGCT
*
1194489 AGTATCGATACTTTTGGGCT
1 AGTATCGATACTCTTGGGCT
1194509 AGTATCGATA
1 AGTATCGATA
1194519 TTTTCAGTCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.36
Consensus pattern (20 bp):
AGTATCGATACTCTTGGGCT
Found at i:1201684 original size:28 final size:27
Alignment explanation
Indices: 1201652--1201744 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 27
1201642 CTTAACAAGC
*
1201652 AACAAATTTTCTTAACAAGCACAAGTCG
1 AACAAATTTT-TTAACAAGCACGAGTCG
* **
1201680 AACAAA-ATTTTAATGAGCAACGAGTCG
1 AACAAATTTTTTAACAAGC-ACGAGTCG
*
1201707 ATA-AATTTTTTTAACAAGCACGAGTCG
1 A-ACAAATTTTTTAACAAGCACGAGTCG
* *
1201734 AGCAAAATTTT
1 AACAAATTTTT
1201745 AATGAGTTTA
Statistics
Matches: 50, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
26 7 0.14
27 27 0.54
28 16 0.32
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (27 bp):
AACAAATTTTTTAACAAGCACGAGTCG
Found at i:1206794 original size:16 final size:16
Alignment explanation
Indices: 1206773--1206803 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1206763 ATGATTAAGC
*
1206773 GCTGAATGATTCAAAT
1 GCTGAATAATTCAAAT
1206789 GCTGAATAATTCAAA
1 GCTGAATAATTCAAA
1206804 AGCTCTGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (16 bp):
GCTGAATAATTCAAAT
Found at i:1207328 original size:27 final size:28
Alignment explanation
Indices: 1207271--1207328 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
1207261 AGAGGTGCAC
*
1207271 AAAAAATTCGAATATCCGATTTTGCGTAA
1 AAAAAATTCGAATATCAGATTTTGCG-AA
* *
1207300 AAAATATTCGAA-ATCAGA-TTTGGGAA
1 AAAAAATTCGAATATCAGATTTTGCGAA
1207326 AAA
1 AAA
1207329 TCGGTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
26 5 0.19
27 5 0.19
28 5 0.19
29 11 0.42
ACGTcount: A:0.47, C:0.10, G:0.16, T:0.28
Consensus pattern (28 bp):
AAAAAATTCGAATATCAGATTTTGCGAA
Found at i:1208618 original size:2 final size:2
Alignment explanation
Indices: 1208611--1208638 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1208601 ATAGCATCTC
1208611 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
1208639 TTGACATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1208659 original size:17 final size:17
Alignment explanation
Indices: 1208637--1208674 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
1208627 ATATATATAT
1208637 ATTTGACATAATAGCTA
1 ATTTGACATAATAGCTA
1208654 ATTTGACATAATAGCTA
1 ATTTGACATAATAGCTA
1208671 ATTT
1 ATTT
1208675 ATACTTGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (17 bp):
ATTTGACATAATAGCTA
Found at i:1209528 original size:2 final size:2
Alignment explanation
Indices: 1209521--1209553 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1209511 TCTATGTATG
1209521 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1209554 TTAACTCTTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1210659 original size:18 final size:16
Alignment explanation
Indices: 1210609--1210662 Score: 58
Period size: 15 Copynumber: 3.3 Consensus size: 16
1210599 CTATAATAAA
1210609 AATAAAAAAT-A-TAT
1 AATAAAAAATAATTAT
1210623 AAATAAAAAATAATTAT
1 -AATAAAAAATAATTAT
*
1210640 AATAAAAATATATTTTAT
1 AATAAAAA-ATA-ATTAT
1210658 AATAA
1 AATAA
1210663 GTCACCATTA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
15 10 0.29
16 9 0.26
17 6 0.18
18 9 0.26
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATAAAAAATAATTAT
Found at i:1217305 original size:35 final size:35
Alignment explanation
Indices: 1217252--1217332 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
1217242 CTCTCACCCA
* * * * *
1217252 TAAATGCTATGTTTGATTTGTTGTTTTTTGGAGAC
1 TAAATGCTATCTTCGATTTGTTATTTTCTGGAAAC
*
1217287 TAAATGCTATCTTCGATTTGTTATTTTCTGGAAAT
1 TAAATGCTATCTTCGATTTGTTATTTTCTGGAAAC
*
1217322 TTAATGCTATC
1 TAAATGCTATC
1217333 ATTTGCTACT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.17, T:0.49
Consensus pattern (35 bp):
TAAATGCTATCTTCGATTTGTTATTTTCTGGAAAC
Found at i:1219829 original size:2 final size:2
Alignment explanation
Indices: 1219824--1219856 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1219814 TATATCTTAC
1219824 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 A
1219857 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1221520 original size:22 final size:21
Alignment explanation
Indices: 1221490--1221552 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 21
1221480 TATAAAAATG
1221490 TAATCTAAATGTGATATTTGTCA
1 TAAT-TAAATGTGATATTT-TCA
* *
1221513 TAATTAAAT-AG-TATTTTAA
1 TAATTAAATGTGATATTTTCA
1221532 TAA-T-AATGTGATATTTATCA
1 TAATTAAATGTGATATTT-TCA
1221552 T
1 T
1221553 CATCAAATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 9
0.72 0.09 0.20
Matches are distributed among these distances:
17 3 0.09
18 2 0.06
19 10 0.30
20 8 0.24
21 1 0.03
22 5 0.15
23 4 0.12
ACGTcount: A:0.40, C:0.05, G:0.10, T:0.46
Consensus pattern (21 bp):
TAATTAAATGTGATATTTTCA
Found at i:1221561 original size:39 final size:39
Alignment explanation
Indices: 1221497--1221576 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
1221487 ATGTAATCTA
* * *
1221497 AATGTGATATTTGTCATAATTAAATAGTATTTTAATAAT
1 AATGTGATATTTATCATAATCAAATAATATTTTAATAAT
*
1221536 AATGTGATATTTATCATCATCAAATAATATTTTAATAAT
1 AATGTGATATTTATCATAATCAAATAATATTTTAATAAT
1221575 AA
1 AA
1221577 GTAATATATG
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (39 bp):
AATGTGATATTTATCATAATCAAATAATATTTTAATAAT
Found at i:1229052 original size:20 final size:20
Alignment explanation
Indices: 1228995--1229053 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
1228985 TGTATAACAT
* *
1228995 ATTTTCTTAAATGATGT-AT
1 ATTTTATTAAATGATGTAAA
* *
1229014 A-TTTATTAAGT-ACTTTAAA
1 ATTTTATTAAATGA-TGTAAA
1229033 ATTTTATTAAATGATGTAAA
1 ATTTTATTAAATGATGTAAA
1229053 A
1 A
1229054 ATTATAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 7
0.70 0.14 0.16
Matches are distributed among these distances:
17 1 0.03
18 10 0.33
19 3 0.10
20 15 0.50
21 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (20 bp):
ATTTTATTAAATGATGTAAA
Found at i:1229086 original size:2 final size:2
Alignment explanation
Indices: 1229081--1229110 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1229071 CTAAAAAATA
1229081 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
1229111 TGAATAGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1233993 original size:53 final size:52
Alignment explanation
Indices: 1233922--1234022 Score: 141
Period size: 53 Copynumber: 1.9 Consensus size: 52
1233912 GAAATTCGAA
* *
1233922 TTTTCTTTGATTAGTTACTTATTTTACTGATA-GTATCCATCATGAAATATGGG
1 TTTTCTTCGATTAATTACTTATTTTAC-GA-ACGTATCCATCATGAAATATGGG
*
1233975 TTTTCTTCGATTAATTACTTATTTTACGAACGGTATCCATCCTGAAAT
1 TTTTCTTCGATTAATTACTTATTTTACGAAC-GTATCCATCATGAAAT
1234023 TTCATTTATA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
51 1 0.02
52 2 0.05
53 40 0.93
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.46
Consensus pattern (52 bp):
TTTTCTTCGATTAATTACTTATTTTACGAACGTATCCATCATGAAATATGGG
Found at i:1239646 original size:28 final size:28
Alignment explanation
Indices: 1239587--1239648 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
1239577 AATAAATATA
* *
1239587 TTTTAACTCGTAATAAAACAATATATCT
1 TTTTAACCCGTAATAAAACAATATATCC
* * *
1239615 TTTTAACCCGTAGTAAAACAATCTCTCC
1 TTTTAACCCGTAATAAAACAATATATCC
1239643 TTTTAA
1 TTTTAA
1239649 TCCAATCTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.37, C:0.19, G:0.05, T:0.39
Consensus pattern (28 bp):
TTTTAACCCGTAATAAAACAATATATCC
Found at i:1241172 original size:25 final size:24
Alignment explanation
Indices: 1241144--1241200 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
1241134 TCTTTAATGT
1241144 ATATTTAATTTGAATTAATT-AAATA
1 ATATTTAATTT--ATTAATTCAAATA
*
1241169 ATATTTTATTTATTAATTCGAAATA
1 ATATTTAATTTATTAATTC-AAATA
1241194 AT-TTTAA
1 ATATTTAA
1241201 AAACCCTAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 7 0.25
24 4 0.14
25 17 0.61
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (24 bp):
ATATTTAATTTATTAATTCAAATA
Found at i:1241176 original size:78 final size:79
Alignment explanation
Indices: 1241027--1241176 Score: 182
Period size: 78 Copynumber: 1.9 Consensus size: 79
1241017 AATAAGTAAG
*
1241027 CATTAAAAGAATGTAATTTATATTACAACTCTTTTAATTGATATATAATTCGGAATAATTAAATA
1 CATTAAAAGAATGTAATTCATATTACAACTCTTTTAATTGATATATAATTCGGAATAATTAAATA
*
1241092 AGTTTTAAAATAAA
66 AATTTTAAAATAAA
* * * * *
1241106 CATT-AAAGATTGTAATTCATATTATAAGTC-TTTAA-TGTATATTTAATT-TGAATTAATTAAA
1 CATTAAAAGAATGTAATTCATATTACAACTCTTTTAATTG-ATATATAATTCGGAA-TAATTAAA
1241167 TAATATTTTA
64 TAA-ATTTTA
1241177 TTTATTAATT
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
76 5 0.08
77 25 0.41
78 27 0.44
79 4 0.07
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.43
Consensus pattern (79 bp):
CATTAAAAGAATGTAATTCATATTACAACTCTTTTAATTGATATATAATTCGGAATAATTAAATA
AATTTTAAAATAAA
Found at i:1241922 original size:19 final size:18
Alignment explanation
Indices: 1241900--1241950 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
1241890 TTTTTAAGAA
1241900 TTATATATATTTTTAAATT
1 TTATATA-ATTTTTAAATT
* *
1241919 TTATAAAATATTTTAATTT
1 TTATATAAT-TTTTAAATT
*
1241938 TTTTATAATTTTT
1 TTATATAATTTTT
1241951 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATATAATTTTTAAATT
Found at i:1242364 original size:2 final size:2
Alignment explanation
Indices: 1242357--1242389 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1242347 CTATAATTTG
1242357 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 A
1242390 AATTATGATA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1245417 original size:6 final size:6
Alignment explanation
Indices: 1245384--1245411 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
1245374 TGTTGTTCGC
1245384 CCCCCT CCCCCT CCCCCT CCCCCT CCCC
1 CCCCCT CCCCCT CCCCCT CCCCCT CCCC
1245412 ACCCCCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.86, G:0.00, T:0.14
Consensus pattern (6 bp):
CCCCCT
Found at i:1248331 original size:20 final size:20
Alignment explanation
Indices: 1248308--1248355 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
1248298 TATCATATCT
1248308 CAAAAATATGATTTTGTATA
1 CAAAAATATGATTTTGTATA
1248328 CAAAAATATGATTTTGTATA
1 CAAAAATATGATTTTGTATA
1248348 CAAAAATA
1 CAAAAATA
1248356 AGCCTTGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.35
Consensus pattern (20 bp):
CAAAAATATGATTTTGTATA
Found at i:1251566 original size:16 final size:17
Alignment explanation
Indices: 1251545--1251580 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
1251535 TTACTATTCA
1251545 TGTGAATAGT-AAATTT
1 TGTGAATAGTAAAATTT
1251561 TGTGAATAGTAAAATTT
1 TGTGAATAGTAAAATTT
1251578 TGT
1 TGT
1251581 CGGCGATACG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.36, C:0.00, G:0.19, T:0.44
Consensus pattern (17 bp):
TGTGAATAGTAAAATTT
Found at i:1258059 original size:32 final size:32
Alignment explanation
Indices: 1258015--1258076 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
1258005 GAGCGTTCAG
*
1258015 TTTATTTAAATTTTAATTGATAAAAATTATAT
1 TTTATTTAAATTTTAATGGATAAAAATTATAT
*
1258047 TTTA-TTATAATTTTAATGGTTAAAAATTAT
1 TTTATTTA-AATTTTAATGGATAAAAATTAT
1258077 TTAGGGATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 3 0.11
32 24 0.89
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (32 bp):
TTTATTTAAATTTTAATGGATAAAAATTATAT
Found at i:1261221 original size:2 final size:2
Alignment explanation
Indices: 1261214--1261247 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1261204 TGAGAACCAA
1261214 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
1261248 TAATTTAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1280463 original size:21 final size:21
Alignment explanation
Indices: 1280439--1280479 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1280429 ATAATTTTGA
*
1280439 TAAAATTAATAGTTTAGATAC
1 TAAAATTAATAATTTAGATAC
*
1280460 TAAAATTTATAATTTAGATA
1 TAAAATTAATAATTTAGATA
1280480 TTAACACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (21 bp):
TAAAATTAATAATTTAGATAC
Found at i:1281082 original size:17 final size:17
Alignment explanation
Indices: 1281051--1281088 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1281041 GTAATTAATC
*
1281051 ATTTTATTATTA-TTTT
1 ATTTTAGTATTATTTTT
1281067 ATTTTAGTATTTATTTTT
1 ATTTTAGTA-TTATTTTT
1281085 ATTT
1 ATTT
1281089 ATTATTTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 8 0.42
17 3 0.16
18 8 0.42
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTTAGTATTATTTTT
Found at i:1283318 original size:30 final size:30
Alignment explanation
Indices: 1283279--1283340 Score: 88
Period size: 30 Copynumber: 2.1 Consensus size: 30
1283269 CAATGTTGTT
*
1283279 GAGATTGATGAGGAAGACGACAACGACGAC
1 GAGAATGATGAGGAAGACGACAACGACGAC
* * *
1283309 GAGAATGATGGGGATGACGACGACGACGAC
1 GAGAATGATGAGGAAGACGACAACGACGAC
1283339 GA
1 GA
1283341 CGATGAGGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.37, T:0.10
Consensus pattern (30 bp):
GAGAATGATGAGGAAGACGACAACGACGAC
Found at i:1284263 original size:27 final size:26
Alignment explanation
Indices: 1284228--1284278 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
1284218 GGTATACTTT
*
1284228 ATGTCATGTTTAATAGTTTGTTGTTAA
1 ATGTAATGTTT-ATAGTTTGTTGTTAA
*
1284255 ATGTAATGTTTATGGTTTGTTGTT
1 ATGTAATGTTTATAGTTTGTTGTT
1284279 TATATAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.22, C:0.02, G:0.22, T:0.55
Consensus pattern (26 bp):
ATGTAATGTTTATAGTTTGTTGTTAA
Found at i:1285255 original size:83 final size:83
Alignment explanation
Indices: 1285159--1285604 Score: 362
Period size: 83 Copynumber: 5.4 Consensus size: 83
1285149 TTTCATAGTG
* * *
1285159 TTTTCTATTATTATTCAGAGAATCTATATCATGTCATAGTGTTCCATCTCATCTGAAATGAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTATCATGTCATAGTGTTCCATCCCATCTGAAATGAAAGG
* * *
1285224 CGCGTTCCAGATGAAGCA
66 CGCATTCCAGAGGAAACA
* * * **
1285242 TTTTCCATTATTATTCAGAGAAACTCT-TCCATGTAATAATGTTTTATCCCATCTGAAATGAAAG
1 TTTTCCATTATTATTCAGAGAATCTCTAT-CATGTCATAGTGTTCCATCCCATCTGAAATGAAAG
** * *
1285306 GTACATTACAGGGGAAACA
65 GCGCATTCCAGAGGAAACA
* * * * * * * ** *
1285325 TTTTTCATTATTATTCAGATAATCTCTGTTATGTCGTAGTATTCAATCCCATCCAAAATAAAAGG
1 TTTTCCATTATTATTCAGAGAATCTCTATCATGTCATAGTGTTCCATCCCATCTGAAATGAAAGG
* * **
1285390 CACTTTCCA-AGAGAAATG
66 CGCATTCCAGAG-GAAACA
* * * * *
1285408 TTTTCCATTATTATTCAGATAATCTCTACCATGTCATAGTG-TACAGTCTCATCCGAAATGAAAG
1 TTTTCCATTATTATTCAGAGAATCTCTATCATGTCATAGTGTTCCA-TCCCATCTGAAATGAAAG
* * * *
1285472 ACGCATTCTAGCGGAAGCA
65 GCGCATTCCAGAGGAAACA
** * * *** * *
1285491 TTTTTTATTATTATTCAGAGAATCTCTGTCATGTCATAATGTTTTGTCCAAT-TGAAATGAAAGA
1 TTTTCCATTATTATTCAGAGAATCTCTATCATGTCATAGTGTTCCATCCCATCTGAAATGAAAGG
* *
1285555 CG-AGTTCCAGGGGAAACG
66 CGCA-TTCCAGAGGAAACA
* *
1285573 TTTTCCATTATTATTCAGAAAATCTCTGTCAT
1 TTTTCCATTATTATTCAGAGAATCTCTATCAT
1285605 TTCACATAAT
Statistics
Matches: 284, Mismatches: 72, Indels: 15
0.77 0.19 0.04
Matches are distributed among these distances:
81 1 0.00
82 56 0.20
83 224 0.79
84 3 0.01
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (83 bp):
TTTTCCATTATTATTCAGAGAATCTCTATCATGTCATAGTGTTCCATCCCATCTGAAATGAAAGG
CGCATTCCAGAGGAAACA
Found at i:1285712 original size:16 final size:16
Alignment explanation
Indices: 1285687--1285731 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
1285677 TTGAAATCTC
1285687 AAACTCTCAAACGTTT-
1 AAACTCTCAAAC-TTTG
*
1285703 AAACTTTCAAACTTTG
1 AAACTCTCAAACTTTG
1285719 AAACTCTCAAACT
1 AAACTCTCAAACT
1285732 AAGAAAACGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 3 0.12
16 23 0.88
ACGTcount: A:0.40, C:0.24, G:0.04, T:0.31
Consensus pattern (16 bp):
AAACTCTCAAACTTTG
Found at i:1290511 original size:13 final size:14
Alignment explanation
Indices: 1290476--1290523 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 14
1290466 TGTGCAGAGG
1290476 TATAAAATT-ATAA
1 TATAAAATTAATAA
* *
1290489 TATTATATTAATAA
1 TATAAAATTAATAA
1290503 -ATAAAATTAATTAA
1 TATAAAATTAA-TAA
1290517 TATAAAA
1 TATAAAA
1290524 ATATTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 15 0.54
14 7 0.25
15 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
TATAAAATTAATAA
Found at i:1290511 original size:18 final size:18
Alignment explanation
Indices: 1290485--1290539 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
1290475 GTATAAAATT
*
1290485 ATAATATTATATTAATAA
1 ATAAAATTATATTAATAA
1290503 ATAAAATTA-ATTAAT--
1 ATAAAATTATATTAATAA
1290518 ATAAAA--ATATTAATAA
1 ATAAAATTATATTAATAA
1290534 GATAAA
1 -ATAAA
1290540 TTTAAATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 9
0.76 0.02 0.21
Matches are distributed among these distances:
13 1 0.03
14 6 0.19
15 6 0.19
17 11 0.34
18 8 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
ATAAAATTATATTAATAA
Found at i:1300344 original size:16 final size:18
Alignment explanation
Indices: 1300308--1300349 Score: 61
Period size: 16 Copynumber: 2.4 Consensus size: 18
1300298 ATATTTTTGT
1300308 TTTATTTTGTTATTAACA
1 TTTATTTTGTTATTAACA
*
1300326 TTTGTTTT-TTATT-ACA
1 TTTATTTTGTTATTAACA
1300342 TTTATTTT
1 TTTATTTT
1300350 AATCACTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 10 0.45
17 5 0.23
18 7 0.32
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTATTTTGTTATTAACA
Found at i:1300965 original size:53 final size:53
Alignment explanation
Indices: 1300896--1301003 Score: 184
Period size: 53 Copynumber: 2.0 Consensus size: 53
1300886 AATTTGTCAA
1300896 GACAATCCGTCTAATTTTTATT-AGTGGTTTAG-TCTCGATCTTTTTAAATAATT
1 GACAATCCGTCTAATTTTTATTAAG-GGTTT-GTTCTCGATCTTTTTAAATAATT
1300949 GACAATCCGTCTAATTTTTATTAAGGGTTTGTTCTCGATCTTTTTAAATAATT
1 GACAATCCGTCTAATTTTTATTAAGGGTTTGTTCTCGATCTTTTTAAATAATT
1301002 GA
1 GA
1301004 GCATCCTTTA
Statistics
Matches: 53, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
52 1 0.02
53 50 0.94
54 2 0.04
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (53 bp):
GACAATCCGTCTAATTTTTATTAAGGGTTTGTTCTCGATCTTTTTAAATAATT
Done.