Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1399
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: 214408
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
File 2 of 2
Found at i:112928 original size:22 final size:23
Alignment explanation
Indices: 112877--112920 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
112867 AAAATTTTTA
*
112877 AATATAATTATAATATTTAAAAAT
1 AATATAAATATAATA-TTAAAAAT
112901 AATATAAATATAATA-TAAAA
1 AATATAAATATAATATTAAAA
112921 TTTATATATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
24 14 0.74
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (23 bp):
AATATAAATATAATATTAAAAAT
Found at i:112929 original size:24 final size:23
Alignment explanation
Indices: 112857--112929 Score: 56
Period size: 24 Copynumber: 2.9 Consensus size: 23
112847 GTAGTAAAAT
112857 ATATAAATATAAAATTTTTAAATATAA
1 ATAT-AATATAAAA--TTT-AATATAA
* * **
112884 TTATAATATTTAAAAATAATATAA
1 ATATAATA-TAAAATTTAATATAA
112908 ATATAATATAAAATTTATATAT
1 ATATAATATAAAATTTA-ATAT
112930 GTGCATTTGA
Statistics
Matches: 36, Mismatches: 8, Indels: 7
0.71 0.16 0.14
Matches are distributed among these distances:
23 6 0.17
24 18 0.50
25 1 0.03
26 4 0.11
27 7 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATAATATAAAATTTAATATAA
Found at i:112989 original size:2 final size:2
Alignment explanation
Indices: 112984--113025 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
112974 GATATATCAC
* *
112984 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113026 TTTTTGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114706 original size:25 final size:24
Alignment explanation
Indices: 114665--114711 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
114655 CGTTAAGGAA
114665 TAAAAATTAAAAATAATTAAATTCT
1 TAAAAATTAAAAATAA-TAAATTCT
*
114690 TAAAAA-TAAATATTAATAAATT
1 TAAAAATTAAA-AATAATAAATT
114712 TGTTTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (24 bp):
TAAAAATTAAAAATAATAAATTCT
Found at i:118920 original size:24 final size:24
Alignment explanation
Indices: 118888--118991 Score: 88
Period size: 24 Copynumber: 4.2 Consensus size: 24
118878 TAATAATGTT
*
118888 ATTAAAATAATAATGTTAAAACTA
1 ATTATAATAATAATGTTAAAACTA
* *
118912 ATTATAATAATAATGTTATAATTA
1 ATTATAATAATAATGTTAAAACTA
* *
118936 ACTTGATGAAT--TTAT-TTAAAAATTTA
1 A-TT-AT-AATAATAATGTT-AAAA-CTA
*
118962 ATTAAAATAATAATGTTAAAACTA
1 ATTATAATAATAATGTTAAAACTA
118986 ATTATA
1 ATTATA
118992 TACTTTTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 16
0.72 0.10 0.18
Matches are distributed among these distances:
23 3 0.05
24 32 0.51
25 17 0.27
26 8 0.13
27 3 0.05
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (24 bp):
ATTATAATAATAATGTTAAAACTA
Found at i:119019 original size:21 final size:21
Alignment explanation
Indices: 118993--119033 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
118983 CTAATTATAT
118993 ACTTTTATATTAAAAAACTAC
1 ACTTTTATATTAAAAAACTAC
* *
119014 ACTTTTATTTTAATAAACTA
1 ACTTTTATATTAAAAAACTA
119034 TCTATTTATC
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:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (21 bp):
ACTTTTATATTAAAAAACTAC
Found at i:120966 original size:14 final size:15
Alignment explanation
Indices: 120942--120971 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
120932 AAATAAAAAT
120942 AAATTATAAATATTA
1 AAATTATAAATATTA
120957 AAATTA-AAATATTA
1 AAATTATAAATATTA
120971 A
1 A
120972 GCTTACTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
AAATTATAAATATTA
Found at i:127899 original size:52 final size:52
Alignment explanation
Indices: 127814--127938 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
127804 ATATGAAAAG
* *
127814 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
127866 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
127918 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
127939 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:127951 original size:52 final size:51
Alignment explanation
Indices: 127814--127958 Score: 211
Period size: 52 Copynumber: 2.8 Consensus size: 51
127804 ATATGAAAAG
*
127814 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* *
127866 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
127918 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
127959 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:127965 original size:13 final size:13
Alignment explanation
Indices: 127947--127971 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
127937 CAAAGATCAG
127947 TGTATCGATACAA
1 TGTATCGATACAA
127960 TGTATCGATACA
1 TGTATCGATACA
127972 TGTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:128761 original size:50 final size:49
Alignment explanation
Indices: 128707--128881 Score: 214
Period size: 50 Copynumber: 3.6 Consensus size: 49
128697 TTAATTTTTA
* *
128707 ACAATCGAGAGAGGTGATTGTAATTGTTGATTATTGTTCACCAACCTTTG
1 ACAATCGAGAGAGGT-ATCGTAATTGTTGACTATTGTTCACCAACCTTTG
*
128757 ACAATCGAGAGAGGTAGGT-GTAATTGTTGACTATTG---ACCAACTTTTG
1 ACAATCGAGAGAGGTA--TCGTAATTGTTGACTATTGTTCACCAACCTTTG
*
128804 ACAATCGAGAGAGGTATCCGTAATTGTTGACTATTCTTCACCAACCTTTG
1 ACAATCGAGAGAGGTAT-CGTAATTGTTGACTATTGTTCACCAACCTTTG
* * *
128854 ATAATAGAGAAAGGTGATCGTAATTGTT
1 ACAATCGAGAGAGGT-ATCGTAATTGTT
128882 AATTCTAAGT
Statistics
Matches: 110, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
45 1 0.01
47 42 0.38
49 1 0.01
50 63 0.57
51 3 0.03
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (49 bp):
ACAATCGAGAGAGGTATCGTAATTGTTGACTATTGTTCACCAACCTTTG
Found at i:128815 original size:47 final size:48
Alignment explanation
Indices: 128702--128838 Score: 170
Period size: 47 Copynumber: 2.8 Consensus size: 48
128692 TTTTATTAAT
* * *
128702 TTTTAACAATCGAGAGAGGT-GATTGTAATTGTTGATTATTGTTCACCAAC
1 TTTTGACAATCGAGAGAGGTAG-CTGTAATTGTTGACTATTG-T-ACCAAC
* *
128752 CTTTGACAATCGAGAGAGGTAGGTGTAATTGTTGACTATTG-ACCAAC
1 TTTTGACAATCGAGAGAGGTAGCTGTAATTGTTGACTATTGTACCAAC
* *
128799 TTTTGACAATCGAGAGAGGTATCCGTAATTGTTGACTATT
1 TTTTGACAATCGAGAGAGGTAGCTGTAATTGTTGACTATT
128839 CTTCACCAAC
Statistics
Matches: 78, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
47 42 0.54
50 35 0.45
51 1 0.01
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (48 bp):
TTTTGACAATCGAGAGAGGTAGCTGTAATTGTTGACTATTGTACCAAC
Found at i:128817 original size:97 final size:97
Alignment explanation
Indices: 128702--128881 Score: 256
Period size: 97 Copynumber: 1.9 Consensus size: 97
128692 TTTTATTAAT
* * * *
128702 TTTTAACAATCGAGAGAGGTGAT-TGTAATTGTTGATTATTGTTCACCAACCTTTGACAATCGAG
1 TTTTAACAATCGAGAGAGGT-ATCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATAGAG
* *
128766 AGAGGTAGGT-GTAATTGTTGACTATTGACCAAC
65 AAAGGT-GATCGTAATTGTTGACTATTGACCAAC
* *
128799 TTTTGACAATCGAGAGAGGTATCCGTAATTGTTGACTATTCTTCACCAACCTTTGATAATAGAGA
1 TTTTAACAATCGAGAGAGGTATCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGA
128864 AAGGTGATCGTAATTGTT
66 AAGGTGATCGTAATTGTT
128882 AATTCTAAGT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
96 4 0.05
97 69 0.95
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.34
Consensus pattern (97 bp):
TTTTAACAATCGAGAGAGGTATCCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATAGAGA
AAGGTGATCGTAATTGTTGACTATTGACCAAC
Found at i:133315 original size:50 final size:50
Alignment explanation
Indices: 133255--133458 Score: 291
Period size: 50 Copynumber: 4.1 Consensus size: 50
133245 GCAAAGCGAT
* * *
133255 TTGATTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGCCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
* * * *
133305 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAAGTGATCATAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
* *
133355 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGCCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
* * * *
133405 TTGACTATTCTTCACCAACCTTTGACAATAGAGAAATGTGACTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
133455 TTGA
1 TTGA
133459 TTTTAAGCAT
Statistics
Matches: 135, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 135 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGACCGTAATTG
Found at i:133453 original size:100 final size:100
Alignment explanation
Indices: 133255--133438 Score: 350
Period size: 100 Copynumber: 1.8 Consensus size: 100
133245 GCAAAGCGAT
*
133255 TTGATTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGCCGTAATTGTTGACTATTCTTCAC
1 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGCCGTAATTGTTGACTATTCTTCAC
*
133320 CAACCTTTGACAATCGAGAGAAGTGATCATAATTA
66 CAACCTTTGACAATAGAGAGAAGTGATCATAATTA
133355 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGCCGTAATTGTTGACTATTCTTCAC
1 TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGCCGTAATTGTTGACTATTCTTCAC
133420 CAACCTTTGACAATAGAGA
66 CAACCTTTGACAATAGAGA
133439 AATGTGACTG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 82 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (100 bp):
TTGACTATTCTTCACCAACCTTTGAGAATCGAGAGAGGTGGCCGTAATTGTTGACTATTCTTCAC
CAACCTTTGACAATAGAGAGAAGTGATCATAATTA
Found at i:135147 original size:42 final size:43
Alignment explanation
Indices: 135082--135170 Score: 121
Period size: 42 Copynumber: 2.1 Consensus size: 43
135072 ATATATAGAA
**
135082 TCATTTATTTTTTTATTTGATAATT-TATATAATTATATTATAT
1 TCATTTATTTTTTTATTTGATAATTATAT-TAAAAATATTATAT
135125 TCATTTA-TTTTTTATATT-ATAATTATATTAAAAATATTATAT
1 TCATTTATTTTTTTAT-TTGATAATTATATTAAAAATATTATAT
135167 TCAT
1 TCAT
135171 ATGTGAAGAT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
42 30 0.71
43 12 0.29
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (43 bp):
TCATTTATTTTTTTATTTGATAATTATATTAAAAATATTATAT
Found at i:136073 original size:2 final size:2
Alignment explanation
Indices: 136066--136098 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
136056 CTAGGCTAAG
136066 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
136099 TTAATACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:137426 original size:97 final size:99
Alignment explanation
Indices: 137290--137485 Score: 333
Period size: 97 Copynumber: 2.0 Consensus size: 99
137280 TCAGACCAGG
*
137290 TGTGAGTATTGGATACGGTATGTGTCCGACACGGATATAGTCAA-TTTTTTTAAAG-TTTTTTCA
1 TGTGAGTATTGGATACGGTATGTGTCCGACAAGGATATAGTCAATTTTTTTTAAAGTTTTTTTCA
* *
137353 TGTATTTGGAGGGTCATATTTTCATACTTATGTT
66 TGTATTTGGAGGGTCATATTTCCATACCTATGTT
* *
137387 TGTGAGTATTGGATATGGTATGTGTCTGACAAGGATATAGTCAATTTTTTTTAAAGTTTTTTTCA
1 TGTGAGTATTGGATACGGTATGTGTCCGACAAGGATATAGTCAATTTTTTTTAAAGTTTTTTTCA
137452 TGTATTTGGAGGGTCATATTTCCATACCTATGTT
66 TGTATTTGGAGGGTCATATTTCCATACCTATGTT
137486 CGAAAATGTG
Statistics
Matches: 92, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
97 41 0.45
98 11 0.12
99 40 0.43
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (99 bp):
TGTGAGTATTGGATACGGTATGTGTCCGACAAGGATATAGTCAATTTTTTTTAAAGTTTTTTTCA
TGTATTTGGAGGGTCATATTTCCATACCTATGTT
Found at i:142629 original size:53 final size:53
Alignment explanation
Indices: 142570--142676 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
142560 CAAACACAAA
*
142570 TGTGAAATATAAATAGTTCTTAAAAAAATAAAAGGTTGGAATAACATATTATG
1 TGTGAAATATAAATAGTTCTTAAAAAAATAAAAGGTCGGAATAACATATTATG
* *
142623 TGTGAAATATAAATAGTTCTTAAAAGAATAAAGGGTCGGAATAACATATTATG
1 TGTGAAATATAAATAGTTCTTAAAAAAATAAAAGGTCGGAATAACATATTATG
142676 T
1 T
142677 TGCTTTTCTA
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.32
Consensus pattern (53 bp):
TGTGAAATATAAATAGTTCTTAAAAAAATAAAAGGTCGGAATAACATATTATG
Found at i:143778 original size:21 final size:20
Alignment explanation
Indices: 143742--143796 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
143732 GTGATAGCGA
*
143742 TGAGATTAATATTATAACAG
1 TGAGATTAAAATTATAACAG
143762 TGAGATTGAAAATTATAACAG
1 TGAGATT-AAAATTATAACAG
* *
143783 TAATATTAAAATTA
1 TGAGATTAAAATTA
143797 ATAAGATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 14 0.45
21 17 0.55
ACGTcount: A:0.49, C:0.04, G:0.13, T:0.35
Consensus pattern (20 bp):
TGAGATTAAAATTATAACAG
Found at i:143837 original size:15 final size:15
Alignment explanation
Indices: 143800--143838 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
143790 AAAATTAATA
**
143800 AGATAATAAATATTT
1 AGATAATAAATACCT
143815 AGAT-ATAAATACCT
1 AGATAATAAATACCT
143829 AGATAATAAA
1 AGATAATAAA
143839 GTAAAAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.56, C:0.05, G:0.08, T:0.31
Consensus pattern (15 bp):
AGATAATAAATACCT
Found at i:144140 original size:18 final size:19
Alignment explanation
Indices: 144119--144158 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
144109 ATATATTTTT
* *
144119 AAATTATTATATAATAA-A
1 AAATTATAATACAATAATA
144137 AAATTATAATACAATAATA
1 AAATTATAATACAATAATA
144156 AAA
1 AAA
144159 ATAAAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATTATAATACAATAATA
Found at i:146351 original size:21 final size:21
Alignment explanation
Indices: 146322--146361 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
146312 ATAAGATTGT
* *
146322 TACTTTAATTGTGAGATTAGA
1 TACTATAATTATGAGATTAGA
146343 TACTATAATTATGAGATTA
1 TACTATAATTATGAGATTA
146362 AGATCAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.42
Consensus pattern (21 bp):
TACTATAATTATGAGATTAGA
Found at i:146501 original size:35 final size:35
Alignment explanation
Indices: 146462--146575 Score: 95
Period size: 35 Copynumber: 3.5 Consensus size: 35
146452 TGTGTATTTA
146462 TATATATATAATAAATAATTAAAAATTATTAAAA-
1 TATATATATAATAAATAATTAAAAATTATTAAAAT
* *
146496 T-TATATAT--TAAATAA-T--AAA--CTTGAAAT
1 TATATATATAATAAATAATTAAAAATTATTAAAAT
* * *
146523 TATATTTATAATAAATAATTAAATATATAGTAAAAT
1 TATATATATAATAAATAATTAAAAAT-TATTAAAAT
*
146559 TATAT-TATATTAAATAA
1 TATATATATAATAAATAA
146576 CAATTGATAA
Statistics
Matches: 62, Mismatches: 8, Indels: 19
0.70 0.09 0.21
Matches are distributed among these distances:
26 5 0.08
27 1 0.02
28 9 0.15
30 8 0.13
31 8 0.13
33 9 0.15
34 1 0.02
35 11 0.18
36 10 0.16
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (35 bp):
TATATATATAATAAATAATTAAAAATTATTAAAAT
Found at i:146542 original size:19 final size:19
Alignment explanation
Indices: 146520--146575 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
146510 ATAAACTTGA
146520 AATTATATTTATAATAAAT
1 AATTATATTTATAATAAAT
* * *
146539 AATTAAATATATAGT-AA-
1 AATTATATTTATAATAAAT
*
146556 AATTATA-TTATATTAAAT
1 AATTATATTTATAATAAAT
146574 AA
1 AA
146576 CAATTGATAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 5 0.17
17 8 0.28
18 4 0.14
19 12 0.41
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AATTATATTTATAATAAAT
Found at i:149319 original size:16 final size:16
Alignment explanation
Indices: 149295--149414 Score: 125
Period size: 16 Copynumber: 7.5 Consensus size: 16
149285 AACTCAAATT
* *
149295 CGAACTGATTTGAACC
1 CGAAATGATTCGAACC
*
149311 CGAAATGATTCGAATC
1 CGAAATGATTCGAACC
* * *
149327 CAAAATAATTCGAATC
1 CGAAATGATTCGAACC
*
149343 CAAAATGATTCGAACC
1 CGAAATGATTCGAACC
*
149359 CGAAATGA-CCTGAACC
1 CGAAATGATTC-GAACC
** *
149375 CGAAATGACCCGAATC
1 CGAAATGATTCGAACC
149391 CGAAATGATTCGAACC
1 CGAAATGATTCGAACC
149407 CGAAATGA
1 CGAAATGA
149415 CCCGAATAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
15 1 0.01
16 86 0.97
17 2 0.02
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (16 bp):
CGAAATGATTCGAACC
Found at i:149512 original size:21 final size:22
Alignment explanation
Indices: 149480--149535 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 22
149470 AAAAAACAAG
*
149480 TTAATAAAATAATAATTATAAA
1 TTAATAATATAATAATTATAAA
* *
149502 TT-ATAATATAA-AATTTTGAA
1 TTAATAATATAATAATTATAAA
*
149522 TTAATTATATAATA
1 TTAATAATATAATA
149536 TGTGATTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 9 0.32
21 16 0.57
22 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAATAATATAATAATTATAAA
Found at i:150504 original size:16 final size:16
Alignment explanation
Indices: 150480--150517 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
150470 CCCGAACTCC
*
150480 AAATGATCCAAACCCG
1 AAATAATCCAAACCCG
*
150496 AAATAATCCGAACCCG
1 AAATAATCCAAACCCG
150512 AAATAA
1 AAATAA
150518 CATGTACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.26, G:0.11, T:0.13
Consensus pattern (16 bp):
AAATAATCCAAACCCG
Found at i:150587 original size:16 final size:17
Alignment explanation
Indices: 150567--150604 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
150557 TCGAAATGAT
150567 CCGAA-CCCAAAATAAC
1 CCGAATCCCAAAATAAC
* *
150583 TCGAATCCGAAAATAAC
1 CCGAATCCCAAAATAAC
150600 CCGAA
1 CCGAA
150605 AATTTTATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.47, C:0.32, G:0.11, T:0.11
Consensus pattern (17 bp):
CCGAATCCCAAAATAAC
Found at i:156467 original size:3 final size:3
Alignment explanation
Indices: 156459--156499 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
156449 ATTCTATGCT
156459 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
156500 ATTATTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:156577 original size:3 final size:3
Alignment explanation
Indices: 156569--156621 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
156559 ATGTTCCAAA
* **
156569 ATT ATT ATT ATT ATT ATT ATT ATT ATC AAA ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
156617 ATT AT
1 ATT AT
156622 CATGCTATTT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:165927 original size:15 final size:16
Alignment explanation
Indices: 165909--165979 Score: 62
Period size: 15 Copynumber: 4.8 Consensus size: 16
165899 TCCTCATTGC
165909 CATAA-TACTTTTTGG
1 CATAAGTACTTTTTGG
165924 CATAAGTAC-TTTTGG
1 CATAAGTACTTTTTGG
*
165939 CACAAGTAC--TTTGG
1 CATAAGTACTTTTTGG
* * *
165953 CACATGTAC-CTTTGG
1 CATAAGTACTTTTTGG
*
165968 CATAGGTACTTT
1 CATAAGTACTTT
165980 GGCACAGGTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
14 13 0.27
15 31 0.65
16 4 0.08
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.38
Consensus pattern (16 bp):
CATAAGTACTTTTTGG
Found at i:166102 original size:27 final size:28
Alignment explanation
Indices: 165919--166437 Score: 299
Period size: 27 Copynumber: 18.8 Consensus size: 28
165909 CATAATACTT
* * *
165919 TTTGGCATAAGTACTTTTGGCACAAGTAC
1 TTTGGCACAGGTAC-TTTGGCACAGGTAC
* *
165948 TTTGGCACATGTACCTTTGGCATAGGTAC
1 TTTGGCACAGGTA-CTTTGGCACAGGTAC
*
165977 TTTGGCACAGGTACTTTTAGCACAGGTACC
1 TTTGGCACAGGTAC-TTTGGCACAGGTA-C
* * * *
166007 TTTGGTATAGGTAC-CTGGCACAGATAC
1 TTTGGCACAGGTACTTTGGCACAGGTAC
* * ** *
166034 TTTGACATAGACACCTTT-G-ACAAGTAC
1 TTTGGCACAGGTA-CTTTGGCACAGGTAC
166061 TTTGGCACAGGTAC-TTGGCACAGGTAC
1 TTTGGCACAGGTACTTTGGCACAGGTAC
* * * *
166088 TTTGGCACAGGTAC-TTAGAACAAGCAC
1 TTTGGCACAGGTACTTTGGCACAGGTAC
** *
166115 TTTGGCACAAATATCTTTGGCACAGATAC
1 TTTGGCACAGGTA-CTTTGGCACAGGTAC
** * * * *
166144 TTTGATAGAAGTAC-TTGGCATAGGTAT
1 TTTGGCACAGGTACTTTGGCACAGGTAC
* * * *
166171 TTTGGCACAAGTACTTTGACATAGATAC
1 TTTGGCACAGGTACTTTGGCACAGGTAC
* * *
166199 -TTGGCATAAGCACTTTGGCACAGGTAC
1 TTTGGCACAGGTACTTTGGCACAGGTAC
* * * *
166226 TTTGGCACAAGTGCTTTAGCATAGGTA-
1 TTTGGCACAGGTACTTTGGCACAGGTAC
* ** *
166253 TTTGGTACAGACACTTTGGCATAGGTAC
1 TTTGGCACAGGTACTTTGGCACAGGTAC
** * **
166281 TTTTGGCACATATACTTTAGCTTAGGTAC
1 -TTTGGCACAGGTACTTTGGCACAGGTAC
* * * ** *
166310 -CTGGCACATGTACTTTAGCTTAAGTAC
1 TTTGGCACAGGTACTTTGGCACAGGTAC
* * *
166337 TTTGGCATAGGTAC-TTGGCACAGGCAT
1 TTTGGCACAGGTACTTTGGCACAGGTAC
* * * * *
166364 TTTGGTATAGGTAC-CTGGCA-TGGTAT
1 TTTGGCACAGGTACTTTGGCACAGGTAC
* *
166390 TTTGGCACAGGTACTTTGCCATAGGTAC
1 TTTGGCACAGGTACTTTGGCACAGGTAC
*
166418 -TTGGCACAGGCACTTTGGCA
1 TTTGGCACAGGTACTTTGGCA
166438 TAAGTACCTT
Statistics
Matches: 381, Mismatches: 93, Indels: 34
0.75 0.18 0.07
Matches are distributed among these distances:
25 2 0.01
26 18 0.05
27 201 0.53
28 59 0.15
29 87 0.23
30 14 0.04
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (28 bp):
TTTGGCACAGGTACTTTGGCACAGGTAC
Found at i:166102 original size:41 final size:42
Alignment explanation
Indices: 165919--166437 Score: 317
Period size: 41 Copynumber: 12.5 Consensus size: 42
165909 CATAATACTT
* * * * *
165919 TTTGGCATAAGTACTTTTGGCACAAGTACTTTGGCACATGTACC
1 TTTGGCACAGGTAC-TTTGGCACAGGTACTTTGGCATAGGTA-C
* * *
165963 TTTGGCATAGGTACTTTGGCACAGGTACTTTTAGCACAGGTACC
1 TTTGGCACAGGTACTTTGGCACAGGTAC-TTTGGCATAGGTA-C
* * * * * **
166007 TTTGGTATAGGTAC-CTGGCACAGATACTTTGACATAGACACC
1 TTTGGCACAGGTACTTTGGCACAGGTACTTTGGCATAGGTA-C
* *
166049 TTT-G-ACAAGTACTTTGGCACAGGTAC-TTGGCACAGGTAC
1 TTTGGCACAGGTACTTTGGCACAGGTACTTTGGCATAGGTAC
* * * * * **
166088 TTTGGCACAGGTAC-TTAGAACAAGCACTTTGGCACAAATATC
1 TTTGGCACAGGTACTTTGGCACAGGTACTTTGGCATAGGTA-C
* ** * * *
166130 TTTGGCACAGATACTTTGATAGAAGTAC-TTGGCATAGGTAT
1 TTTGGCACAGGTACTTTGGCACAGGTACTTTGGCATAGGTAC
* * * * * *
166171 TTTGGCACAAGTACTTTGACATAGATAC-TTGGCATAAGCAC
1 TTTGGCACAGGTACTTTGGCACAGGTACTTTGGCATAGGTAC
* * *
166212 TTTGGCACAGGTACTTTGGCACAAGTGCTTTAGCATAGGTA-
1 TTTGGCACAGGTACTTTGGCACAGGTACTTTGGCATAGGTAC
* ** * * **
166253 TTTGGTACAGACACTTTGGCATAGGTACTTTTGGCACATATAC
1 TTTGGCACAGGTACTTTGGCACAGGTAC-TTTGGCATAGGTAC
* ** * * * * *
166296 TTTAGCTTAGGTAC-CTGGCACATGTACTTTAGCTTAAGTAC
1 TTTGGCACAGGTACTTTGGCACAGGTACTTTGGCATAGGTAC
* * * *
166337 TTTGGCATAGGTAC-TTGGCACAGGCATTTTGGTATAGGTAC
1 TTTGGCACAGGTACTTTGGCACAGGTACTTTGGCATAGGTAC
* * * *
166378 -CTGGCA-TGGTATTTTGGCACAGGTACTTTGCCATAGGTAC
1 TTTGGCACAGGTACTTTGGCACAGGTACTTTGGCATAGGTAC
*
166418 -TTGGCACAGGCACTTTGGCA
1 TTTGGCACAGGTACTTTGGCA
166438 TAAGTACCTT
Statistics
Matches: 363, Mismatches: 100, Indels: 27
0.74 0.20 0.06
Matches are distributed among these distances:
39 8 0.02
40 57 0.16
41 155 0.43
42 64 0.18
43 40 0.11
44 39 0.11
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (42 bp):
TTTGGCACAGGTACTTTGGCACAGGTACTTTGGCATAGGTAC
Found at i:166407 original size:14 final size:14
Alignment explanation
Indices: 165919--166437 Score: 299
Period size: 14 Copynumber: 37.5 Consensus size: 14
165909 CATAATACTT
* *
165919 TTTGGCATAAGTAC
1 TTTGGCACAGGTAC
*
165933 TTTTGGCACAAGTAC
1 -TTTGGCACAGGTAC
*
165948 TTTGGCACATGTACC
1 TTTGGCACAGGTA-C
*
165963 TTTGGCATAGGTAC
1 TTTGGCACAGGTAC
165977 TTTGGCACAGGTAC
1 TTTGGCACAGGTAC
*
165991 TTTTAGCACAGGTACC
1 -TTTGGCACAGGTA-C
* *
166007 TTTGGTATAGGTAC
1 TTTGGCACAGGTAC
* *
166021 -CTGGCACAGATAC
1 TTTGGCACAGGTAC
* * **
166034 TTTGACATAGACACC
1 TTTGGCACAGGTA-C
*
166049 TTT-G-ACAAGTAC
1 TTTGGCACAGGTAC
166061 TTTGGCACAGGTAC
1 TTTGGCACAGGTAC
166075 -TTGGCACAGGTAC
1 TTTGGCACAGGTAC
166088 TTTGGCACAGGTAC
1 TTTGGCACAGGTAC
* * * *
166102 -TTAGAACAAGCAC
1 TTTGGCACAGGTAC
**
166115 TTTGGCACAAATATC
1 TTTGGCACAGGTA-C
*
166130 TTTGGCACAGATAC
1 TTTGGCACAGGTAC
** * *
166144 TTTGATAGAAGTAC
1 TTTGGCACAGGTAC
* *
166158 -TTGGCATAGGTAT
1 TTTGGCACAGGTAC
*
166171 TTTGGCACAAGTAC
1 TTTGGCACAGGTAC
* * *
166185 TTTGACATAGATAC
1 TTTGGCACAGGTAC
* * *
166199 -TTGGCATAAGCAC
1 TTTGGCACAGGTAC
166212 TTTGGCACAGGTAC
1 TTTGGCACAGGTAC
* *
166226 TTTGGCACAAGTGC
1 TTTGGCACAGGTAC
* *
166240 TTTAGCATAGGTA-
1 TTTGGCACAGGTAC
* **
166253 TTTGGTACAGACAC
1 TTTGGCACAGGTAC
*
166267 TTTGGCATAGGTAC
1 TTTGGCACAGGTAC
**
166281 TTTTGGCACATATAC
1 -TTTGGCACAGGTAC
* **
166296 TTTAGCTTAGGTAC
1 TTTGGCACAGGTAC
* *
166310 -CTGGCACATGTAC
1 TTTGGCACAGGTAC
* ** *
166323 TTTAGCTTAAGTAC
1 TTTGGCACAGGTAC
*
166337 TTTGGCATAGGTAC
1 TTTGGCACAGGTAC
* *
166351 -TTGGCACAGGCAT
1 TTTGGCACAGGTAC
* *
166364 TTTGGTATAGGTAC
1 TTTGGCACAGGTAC
* * *
166378 -CTGGCA-TGGTAT
1 TTTGGCACAGGTAC
166390 TTTGGCACAGGTAC
1 TTTGGCACAGGTAC
* *
166404 TTTGCCATAGGTAC
1 TTTGGCACAGGTAC
*
166418 -TTGGCACAGGCAC
1 TTTGGCACAGGTAC
166431 TTTGGCA
1 TTTGGCA
166438 TAAGTACCTT
Statistics
Matches: 374, Mismatches: 111, Indels: 39
0.71 0.21 0.07
Matches are distributed among these distances:
12 8 0.02
13 97 0.26
14 193 0.52
15 75 0.20
16 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.32
Consensus pattern (14 bp):
TTTGGCACAGGTAC
Found at i:172167 original size:28 final size:28
Alignment explanation
Indices: 172124--172179 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
172114 CGCACAAAGT
172124 CTTGGCATGCAGCATGAAAAACATGTTA
1 CTTGGCATGCAGCATGAAAAACATGTTA
* *
172152 CTTGGCATGTATCATGAAAAACATGTTA
1 CTTGGCATGCAGCATGAAAAACATGTTA
172180 TTTATTTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (28 bp):
CTTGGCATGCAGCATGAAAAACATGTTA
Found at i:172682 original size:63 final size:65
Alignment explanation
Indices: 172614--172773 Score: 182
Period size: 67 Copynumber: 2.5 Consensus size: 65
172604 GTAGCATATA
** *
172614 AGACCATAATCGTCGACTTCTTTATT-AAGT-GTGTAAATGAGAAAGTGATAGGAGTGGCACAGG
1 AGACCATAATCGTCGACTTCTCCATTAAAATAGTGTAAATGAGAAAGTGATAGGAGTGGCACAGG
* * * *
172677 AGACCATAATGGTCGACTTCTCCATTAAAAATACTTGTAAATGAGAGAGTGATAGGAGTGGCGCA
1 AGACCATAATCGTCGACTTCTCCATT-AAAATA-GTGTAAATGAGAAAGTGATAGGAGTGGCACA
*
172742 TG
64 GG
* *
172744 AGACCACAA-CGGTCGACTTTTCCATTAAAA
1 AGACCATAATC-GTCGACTTCTCCATTAAAA
172774 GAATTTGTAC
Statistics
Matches: 81, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
63 23 0.28
65 3 0.04
66 4 0.05
67 51 0.63
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.26
Consensus pattern (65 bp):
AGACCATAATCGTCGACTTCTCCATTAAAATAGTGTAAATGAGAAAGTGATAGGAGTGGCACAGG
Found at i:172737 original size:67 final size:67
Alignment explanation
Indices: 172645--172905 Score: 251
Period size: 67 Copynumber: 3.9 Consensus size: 67
172635 TTATTAAGTG
* *
172645 TGTAAATGAGAAAGTGATAGGAGTGGCACAGGAGACCATAATGGTCGACTTCTCCATTAAAAATA
1 TGTAAATGAGAAAGTGATAGGAGTGGCACAGGAGACCATAACGGTCGACTTTTCCATTAAAAATA
*
172710 CT
66 TT
* * * *
172712 TGTAAATGAGAGAGTGATAGGAGTGGCGCATGAGACCACAACGGTCGACTTTTCCATTAAAAGA-
1 TGTAAATGAGAAAGTGATAGGAGTGGCACAGGAGACCATAACGGTCGACTTTTCCATTAAAA-AT
172776 ATT
65 ATT
* * * * * * *
172779 TGTACAT-ACGGAGAGTGATAGAAGTGATGCA-TGG-GGCCATAATGGTCGACTTTTCCATTAAG
1 TGTAAATGA--GAAAGTGATAGGAGTG--GCACAGGAGACCATAACGGTCGACTTTTCCATTAAA
*
172841 AGTATT
62 AATATT
* * * * * * *
172847 TGTAAATAAGAAAGTGATGGGAGTGGCATAAGAGATCATAACAGTCGACTTTTCTATTA
1 TGTAAATGAGAAAGTGATAGGAGTGGCACAGGAGACCATAACGGTCGACTTTTCCATTA
172906 TTAGTACATG
Statistics
Matches: 157, Mismatches: 28, Indels: 18
0.77 0.14 0.09
Matches are distributed among these distances:
65 3 0.02
66 2 0.01
67 98 0.62
68 50 0.32
69 2 0.01
70 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.26
Consensus pattern (67 bp):
TGTAAATGAGAAAGTGATAGGAGTGGCACAGGAGACCATAACGGTCGACTTTTCCATTAAAAATA
TT
Found at i:175485 original size:14 final size:14
Alignment explanation
Indices: 175451--175526 Score: 66
Period size: 14 Copynumber: 5.6 Consensus size: 14
175441 ACTATGTCAT
*
175451 ATACCTATGCCAAA
1 ATACCTGTGCCAAA
175465 ATACCTGTGCCAAA
1 ATACCTGTGCCAAA
* *
175479 ATACCTGT-ACTAA
1 ATACCTGTGCCAAA
* * **
175492 GTAACTGTATCAAA
1 ATACCTGTGCCAAA
*
175506 GTACCTGTGCC-AA
1 ATACCTGTGCCAAA
175519 ATACCTGT
1 ATACCTGT
175527 ATCATACATT
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
13 18 0.36
14 32 0.64
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (14 bp):
ATACCTGTGCCAAA
Found at i:175526 original size:27 final size:27
Alignment explanation
Indices: 175451--175530 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 27
175441 ACTATGTCAT
* **
175451 ATACCTATGCCAAAATACCTGTGCCAAA
1 ATACCTGTGCC-AAATACCTGTATCAAA
* * * *
175479 ATACCTGTACTAAGTAACTGTATCAAA
1 ATACCTGTGCCAAATACCTGTATCAAA
*
175506 GTACCTGTGCCAAATACCTGTATCA
1 ATACCTGTGCCAAATACCTGTATCA
175531 TACATTATTA
Statistics
Matches: 40, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
27 32 0.80
28 8 0.20
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.26
Consensus pattern (27 bp):
ATACCTGTGCCAAATACCTGTATCAAA
Found at i:175689 original size:44 final size:44
Alignment explanation
Indices: 175639--175722 Score: 136
Period size: 44 Copynumber: 1.9 Consensus size: 44
175629 TCCCCCCGCT
175639 ATTATATTATTCATT-ATTTATTAATATGA-TATTAATTATTAAAC
1 ATTATATTA-TCATTAATTTATTAATAT-ATTATTAATTATTAAAC
175683 ATTATATTATCATTAATTTATTAATATATTATTAATTATT
1 ATTATATTATCATTAATTTATTAATATATTATTAATTATT
175723 TTTTATATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
43 6 0.16
44 32 0.84
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (44 bp):
ATTATATTATCATTAATTTATTAATATATTATTAATTATTAAAC
Found at i:175735 original size:21 final size:21
Alignment explanation
Indices: 175706--175766 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
175696 TAATTTATTA
*
175706 ATATATTATTAATTATTTTTT
1 ATATGTTATTAATTATTTTTT
* * *
175727 ATATGTTATCAATCATTTATT
1 ATATGTTATTAATTATTTTTT
175748 ACT-TCGTTATTAATT-TTTT
1 A-TAT-GTTATTAATTATTTT
175767 ACTACTTTTA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.61
Consensus pattern (21 bp):
ATATGTTATTAATTATTTTTT
Found at i:176552 original size:109 final size:104
Alignment explanation
Indices: 176322--176624 Score: 338
Period size: 109 Copynumber: 2.8 Consensus size: 104
176312 TATATTTATA
* * *
176322 TAGACTCTATTTTTAAATATTTAGTAATTTAAATTTAAATAAATTAATAAAATTACATATTGAAA
1 TAGACTCTATTTTTAAATATTTATTAATTTAAATTTAAATAAAATAATAAAATGACATATTGAAA
** * *
176387 TCTGAAATTTTATTAATTTTAACGTAGATTAATATAATG
66 TAAGAAATTTTATTAATTTTAAAGTAAATTAATATAATG
* * * * * *
176426 CAAACTTTATTTTTAAATATTTATTAATTTAGATTTAAATTTTAAAATAATAAAATGATATATTT
1 TAGACTCTATTTTTAAATATTTATTAATTTAAATTTAAA---TAAAATAATAAAATGACATATTG
* *
176491 TAATAAGAAAATTTTTATTAATTTTAAAGTAAATTAATATCATG
63 AAATAAG-AAA-TTTTATTAATTTTAAAGTAAATTAATATAATG
* * *
176535 TAGACTCTATTTTTAAATATTTATTAATTTAAATTTAAA-AAATTTTAATAAAATTACATATTTA
1 TAGACTCTATTTTTAAATATTTATTAATTTAAATTTAAATAAA--ATAATAAAATGACATATTGA
* * *
176599 AGTAGGATAACTTTATTAATTTTAAA
64 AATAAGA-AATTTTATTAATTTTAAA
176625 ATTTTAAAAA
Statistics
Matches: 165, Mismatches: 26, Indels: 14
0.80 0.13 0.07
Matches are distributed among these distances:
104 34 0.21
105 3 0.02
106 16 0.10
107 45 0.27
108 3 0.02
109 64 0.39
ACGTcount: A:0.45, C:0.04, G:0.05, T:0.46
Consensus pattern (104 bp):
TAGACTCTATTTTTAAATATTTATTAATTTAAATTTAAATAAAATAATAAAATGACATATTGAAA
TAAGAAATTTTATTAATTTTAAAGTAAATTAATATAATG
Found at i:179929 original size:32 final size:34
Alignment explanation
Indices: 179853--179934 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 34
179843 TTATCAGATA
* *
179853 TATATTTAAATAAATAAAAATATAAAAATATAATT
1 TATA-TTAAATATATAAAAAAATAAAAATATAATT
* * *
179888 TTTA-AAAATATATAAAAAAAT-TAAATAT-ATT
1 TATATTAAATATATAAAAAAATAAAAATATAATT
179919 TATATTAAATATATAA
1 TATATTAAATATATAA
179935 TTATATTTGA
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
31 6 0.15
32 16 0.41
33 14 0.36
35 3 0.08
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (34 bp):
TATATTAAATATATAAAAAAATAAAAATATAATT
Found at i:179947 original size:17 final size:17
Alignment explanation
Indices: 179893--179941 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
179883 TAATTTTTAA
** *
179893 AAATATATAAAAAAATT
1 AAATATATAATTATATT
179910 AAATATAT--TTATATT
1 AAATATATAATTATATT
179925 AAATATATAATTATATT
1 AAATATATAATTATATT
179942 TGATATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 12 0.44
17 15 0.56
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATATATAATTATATT
Found at i:181001 original size:26 final size:26
Alignment explanation
Indices: 180971--181020 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
180961 GTGAATATGC
* *
180971 TTTATTTGGTATTGGGTTTAGATGGT
1 TTTATTTGGTAATGCGTTTAGATGGT
180997 TTTATTTGGTAATGCGTTTAGATG
1 TTTATTTGGTAATGCGTTTAGATG
181021 ACATGAGCAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.18, C:0.02, G:0.28, T:0.52
Consensus pattern (26 bp):
TTTATTTGGTAATGCGTTTAGATGGT
Found at i:182187 original size:18 final size:19
Alignment explanation
Indices: 182148--182187 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
182138 TAATTTTTTA
*
182148 TTTTTTATATTCATTTTCT
1 TTTTTTATATTCATTCTCT
182167 TTTTTTAT-TTC-TTCTCT
1 TTTTTTATATTCATTCTCT
182184 TTTT
1 TTTT
182188 CGTTTTTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 3 0.15
19 8 0.40
ACGTcount: A:0.10, C:0.12, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTTTATATTCATTCTCT
Found at i:182368 original size:17 final size:17
Alignment explanation
Indices: 182342--182384 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
182332 TTTCTTTCTT
*
182342 TTTTCTTTTTAATTTCA
1 TTTTCATTTTAATTTCA
*
182359 TTTTCATTTTCATTTCA
1 TTTTCATTTTAATTTCA
182376 -TTTCATTTT
1 TTTTCATTTT
182385 TTCTTCTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTCATTTTAATTTCA
Found at i:182570 original size:19 final size:19
Alignment explanation
Indices: 182546--182582 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
182536 CCTTCCTTTT
182546 TTTCTCTCTAT-CAATTGTC
1 TTTCTCTC-ATCCAATTGTC
182565 TTTCTCTCATCCAATTGT
1 TTTCTCTCATCCAATTGT
182583 GTGTGGTGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.16, C:0.27, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTCTCTCATCCAATTGTC
Found at i:182760 original size:20 final size:20
Alignment explanation
Indices: 182735--182773 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
182725 AAGAATTGAA
182735 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAT
**
182755 GAGGGATACTTGAGAGGGA
1 GAGGGATACAAGAGAGGGA
182774 GGATGGAGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.46, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAT
Found at i:182917 original size:27 final size:27
Alignment explanation
Indices: 182856--182926 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
182846 AAACAAGCCT
* *
182856 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
*
182884 CTATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
182911 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
182927 AATGGGTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:184846 original size:21 final size:22
Alignment explanation
Indices: 184808--184853 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
184798 ATCTGTTGAA
* **
184808 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
184829 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
184851 ACT
1 ACT
184854 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:187333 original size:20 final size:20
Alignment explanation
Indices: 187308--187350 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
187298 AATTGAAAAA
*
187308 GGATACAAGAGAGGGATGAG
1 GGATACAAGAGAGGGAGGAG
**
187328 GGATACTTGAGAGGGAGGAG
1 GGATACAAGAGAGGGAGGAG
187348 GGA
1 GGA
187351 GCCTCTATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.49, T:0.12
Consensus pattern (20 bp):
GGATACAAGAGAGGGAGGAG
Found at i:187488 original size:27 final size:28
Alignment explanation
Indices: 187432--187497 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 28
187422 AGCCTCTATA
*
187432 TTTGACAAATACAAAAGAAACCACCATT
1 TTTGACAAACACAAAAGAAACCACCATT
*
187460 TTTGACAAACACAAAA-TAACCACCATT
1 TTTGACAAACACAAAAGAAACCACCATT
187487 TTTGACAAACA
1 TTTGACAAACA
187498 AATGGGTGGC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
27 21 0.58
28 15 0.42
ACGTcount: A:0.48, C:0.23, G:0.06, T:0.23
Consensus pattern (28 bp):
TTTGACAAACACAAAAGAAACCACCATT
Found at i:188201 original size:33 final size:33
Alignment explanation
Indices: 188156--188225 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
188146 ATATATTTTT
** *
188156 TTATTTTAAATTTAATAATATTTGAGATAAATA
1 TTATTTTAAATTTAATAATATTAAAAATAAATA
*
188189 TTATTTTTAATTTAATAATATTAAAAATAAATA
1 TTATTTTAAATTTAATAATATTAAAAATAAATA
188222 TTAT
1 TTAT
188226 CGTCAAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (33 bp):
TTATTTTAAATTTAATAATATTAAAAATAAATA
Found at i:188210 original size:17 final size:17
Alignment explanation
Indices: 188157--188210 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
188147 TATATTTTTT
188157 TATTTTAAATTTAATAA
1 TATTTTAAATTTAATAA
* * * *
188174 TATTTGAGA-TAAATAT
1 TATTTTAAATTTAATAA
*
188190 TATTTTTAATTTAATAA
1 TATTTTAAATTTAATAA
188207 TATT
1 TATT
188211 AAAAATAAAT
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
16 11 0.41
17 16 0.59
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TATTTTAAATTTAATAA
Found at i:190761 original size:17 final size:17
Alignment explanation
Indices: 190739--190776 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
190729 TAAAAAAATT
*
190739 ATATATATTTATATTGA
1 ATATATAATTATATTGA
*
190756 ATATATAATTATATTTA
1 ATATATAATTATATTGA
190773 ATAT
1 ATAT
190777 TATCTGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATATATAATTATATTGA
Found at i:195559 original size:38 final size:38
Alignment explanation
Indices: 195474--195562 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
195464 TAATTGTATT
* *
195474 ATAACTATTTAT--TTAATATAATTGTTGATATTATGAA
1 ATAATTATTTATAATTAATATAATTGTT-ATATAATGAA
*
195511 ATAATTATTTATAATTAATATAATTG-TATTATAATTAA
1 ATAATTATTTATAATTAATATAATTGTTA-TATAATGAA
195549 ATAATTATTTATAA
1 ATAATTATTTATAA
195563 AATTTATCAT
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
37 12 0.26
38 22 0.48
39 12 0.26
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (38 bp):
ATAATTATTTATAATTAATATAATTGTTATATAATGAA
Found at i:195566 original size:20 final size:18
Alignment explanation
Indices: 195509--195562 Score: 81
Period size: 19 Copynumber: 2.9 Consensus size: 18
195499 TGATATTATG
195509 AAATAATTATTTATAATT
1 AAATAATTATTTATAATT
*
195527 AATATAATTGTATTATAATT
1 AA-ATAATTAT-TTATAATT
195547 AAATAATTATTTATAA
1 AAATAATTATTTATAA
195563 AATTTATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.25
19 14 0.44
20 10 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AAATAATTATTTATAATT
Found at i:195579 original size:27 final size:27
Alignment explanation
Indices: 195549--195615 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
195539 TTATAATTAA
*
195549 ATAATTATTTATAAAATTTATCAT-TTT
1 ATAATTATTTATAAAA-TAATCATGTTT
* *
195576 ATAATTATTTTTAAAATAATTATGTTT
1 ATAATTATTTATAAAATAATCATGTTT
195603 ATAATTAATTTAT
1 ATAATT-ATTTAT
195616 TATTTCTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 5 0.15
27 24 0.71
28 5 0.15
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (27 bp):
ATAATTATTTATAAAATAATCATGTTT
Found at i:195860 original size:15 final size:17
Alignment explanation
Indices: 195842--195876 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
195832 ATTATTTTTT
195842 ATATTTTT-ATT-TAAA
1 ATATTTTTAATTATAAA
195857 ATATTTTTAATTATAAA
1 ATATTTTTAATTATAAA
195874 ATA
1 ATA
195877 ATAAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 8 0.44
16 3 0.17
17 7 0.39
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATTTTTAATTATAAA
Found at i:196099 original size:11 final size:11
Alignment explanation
Indices: 196083--196125 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
196073 AGAACTAGTT
*
196083 AAAAAATGAAA
1 AAAAAAAGAAA
196094 AAAAAAAGAAAA
1 AAAAAAAG-AAA
196106 AAGAAAAAGAAA
1 AA-AAAAAGAAA
196118 AATAAAAA
1 AA-AAAAA
196126 ATATATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 7 0.25
12 15 0.54
13 6 0.21
ACGTcount: A:0.86, C:0.00, G:0.09, T:0.05
Consensus pattern (11 bp):
AAAAAAAGAAA
Found at i:196107 original size:13 final size:13
Alignment explanation
Indices: 196091--196126 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
196081 TTAAAAAATG
196091 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
*
196104 AAAAGAAAAAGAA
1 AAAAAAAAAAGAA
196117 AAATAAAAAA
1 AAA-AAAAAA
196127 TATATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.89, C:0.00, G:0.08, T:0.03
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:196568 original size:18 final size:17
Alignment explanation
Indices: 196545--196588 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
196535 TTGATAGTAA
*
196545 TTAAAAATAATTTTATAG
1 TTAAAAATAATTTT-GAG
196563 TTAAAAAT-ATTTTGAG
1 TTAAAAATAATTTTGAG
*
196579 TAAAAAATAA
1 TTAAAAATAA
196589 AAGAAAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.39
17 6 0.26
18 8 0.35
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (17 bp):
TTAAAAATAATTTTGAG
Found at i:197618 original size:21 final size:22
Alignment explanation
Indices: 197594--197640 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
197584 ATTATATTTT
*
197594 ATAAATT-AATAATTTTTAAAA
1 ATAAATTAAATAATTATTAAAA
* *
197615 ATAATTTAAATTATTATTAAAA
1 ATAAATTAAATAATTATTAAAA
197637 ATAA
1 ATAA
197641 TCTCAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATAAATTAAATAATTATTAAAA
Found at i:202315 original size:11 final size:11
Alignment explanation
Indices: 202250--202315 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
202240 CACGTATATT
202250 TATATTTAATA
1 TATATTTAATA
*
202261 TTTATTTAATA
1 TATATTTAATA
**
202272 TATAAATAATA
1 TATATTTAATA
**
202283 TAATATAAAATA
1 T-ATATTTAATA
*
202295 TTTTTATTTAATA
1 --TATATTTAATA
202308 TATATTTA
1 TATATTTA
202316 TACATATAAT
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
11 26 0.62
12 8 0.19
13 7 0.17
14 1 0.02
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATATTTAATA
Found at i:202781 original size:25 final size:24
Alignment explanation
Indices: 202753--202815 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 24
202743 TTTAAATTCA
202753 ATAAT-TTTAAATATAATATAAAATT
1 ATAATATTT-AATA-AATATAAAATT
202778 ATAATATTTAATAAATATAAAA--
1 ATAATATTTAATAAATATAAAATT
*
202800 ATAATATATAATAAAT
1 ATAATATTTAATAAAT
202816 TTAATTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
22 15 0.42
24 9 0.25
25 9 0.25
26 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAATATTTAATAAATATAAAATT
Found at i:203973 original size:23 final size:23
Alignment explanation
Indices: 203939--203982 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
203929 TATCTTTCAA
203939 ATATATAAATAT-TTTAATATAAT
1 ATATATAAATATATTT-ATATAAT
*
203962 ATATATATATATATTTATATA
1 ATATATAAATATATTTATATA
203983 GAATACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATATATAAATATATTTATATAAT
Found at i:203987 original size:25 final size:23
Alignment explanation
Indices: 203939--203987 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 23
203929 TATCTTTCAA
*
203939 ATATATAAATATTTTAATATAAT
1 ATATATAAATATTTTAATAGAAT
*
203962 ATATATATATATATTTATATAGAAT
1 ATATATAAATAT-TTTA-ATAGAAT
203987 A
1 A
203988 CATTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 11 0.50
24 4 0.18
25 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATATAAATATTTTAATAGAAT
Found at i:204694 original size:16 final size:16
Alignment explanation
Indices: 204648--204694 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
204638 TTTATATTTA
*
204648 AAAT-TAAATATATATT
1 AAATATAAATAT-TTTT
204664 AAATATAAA-ATTTTT
1 AAATATAAATATTTTT
204679 AAATATAAATATTTTT
1 AAATATAAATATTTTT
204695 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 12 0.43
16 12 0.43
17 4 0.14
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATATAAATATTTTT
Found at i:205775 original size:2 final size:2
Alignment explanation
Indices: 205770--205808 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
205760 GAGAGAAAAT
205770 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
205809 GATTACAGGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:206861 original size:21 final size:22
Alignment explanation
Indices: 206808--206862 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
206798 ACAATTTTTT
206808 TAATAAAATTAAAATTCTTATTA
1 TAATAAAA-TAAAATTCTTATTA
*
206831 TAAATTAAATAAAA-T-TTATTAA
1 T-AATAAAATAAAATTCTTATT-A
206853 TAATAAAATA
1 TAATAAAATA
206863 TTTACAATAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
21 13 0.46
22 3 0.11
23 6 0.21
24 6 0.21
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TAATAAAATAAAATTCTTATTA
Found at i:208147 original size:22 final size:22
Alignment explanation
Indices: 208112--208154 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
208102 ATATTTTATT
208112 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAATATA
208134 TAAATATTAA-TATAAAAATAT
1 TAAAT-TTAATTATAAAAATAT
208155 TTTTTAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TAAATTTAATTATAAAAATATA
Found at i:212235 original size:2 final size:2
Alignment explanation
Indices: 212228--212259 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
212218 GGTAGCGGAT
212228 CA CA CA CA CA CA CA CA CA CA C- CA CA -A CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
212260 TATATATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:213141 original size:26 final size:26
Alignment explanation
Indices: 213111--213211 Score: 107
Period size: 26 Copynumber: 3.9 Consensus size: 26
213101 TACTAAAACA
* *
213111 TTATAAATACATAAATATTTTAAAAT
1 TTATAAATATATAAATATATTAAAAT
* *
213137 TTATAAATATAAAAATAATATTAAAACA
1 TTATAAATATATAAAT-ATATTAAAA-T
* * *
213165 TTATGAATATACAAATATCTTAAAAT
1 TTATAAATATATAAATATATTAAAAT
213191 TTATAAA-ATATAAAT-TATTAA
1 TTATAAATATATAAATATATTAA
213212 CGTATCAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
24 5 0.08
25 7 0.11
26 20 0.32
27 16 0.26
28 14 0.23
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (26 bp):
TTATAAATATATAAATATATTAAAAT
Found at i:213173 original size:28 final size:27
Alignment explanation
Indices: 213093--213211 Score: 102
Period size: 27 Copynumber: 4.5 Consensus size: 27
213083 AGTCGATAGA
* *
213093 AAAAATAATACTAAAACATTATAAATAC
1 AAAAAT-ATATTAAAACATTATAAATAT
* * *
213121 ATAAATATTTTAAAA-TTTATAAATAT
1 AAAAATATATTAAAACATTATAAATAT
*
213147 AAAAATAATATTAAAACATTATGAATAT
1 AAAAAT-ATATTAAAACATTATAAATAT
* * *
213175 ACAAATATCTTAAAA-TTTATAAA-AT
1 AAAAATATATTAAAACATTATAAATAT
*
213200 ATAAAT-TATTAA
1 AAAAATATATTAA
213212 CGTATCAAAT
Statistics
Matches: 74, Mismatches: 15, Indels: 8
0.76 0.15 0.08
Matches are distributed among these distances:
24 5 0.07
25 7 0.09
26 20 0.27
27 23 0.31
28 19 0.26
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (27 bp):
AAAAATATATTAAAACATTATAAATAT
Found at i:213181 original size:54 final size:55
Alignment explanation
Indices: 213093--213204 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 55
213083 AGTCGATAGA
* *
213093 AAAAATAATACTAAAACATTATAAATACATAAATATTTTAAAATTTAT-AAATAT
1 AAAAATAATACTAAAACATTATAAATACACAAATATCTTAAAATTTATAAAATAT
* * *
213147 AAAAATAATATTAAAACATTATGAATATACAAATATCTTAAAATTTATAAAATAT
1 AAAAATAATACTAAAACATTATAAATACACAAATATCTTAAAATTTATAAAATAT
213202 AAA
1 AAA
213205 TTATTAACGT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
54 43 0.83
55 9 0.17
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.34
Consensus pattern (55 bp):
AAAAATAATACTAAAACATTATAAATACACAAATATCTTAAAATTTATAAAATAT
Found at i:213276 original size:17 final size:16
Alignment explanation
Indices: 213245--213278 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
213235 AAATACTTTA
*
213245 AATATAATTATAATAT
1 AATAAAATTATAATAT
213261 AATAAAATTCATAATAT
1 AATAAAATT-ATAATAT
213278 A
1 A
213279 CATGTATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
AATAAAATTATAATAT
Done.