Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13
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: 46006518
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2011935 characters in sequence are not A, C, G, or T
File 10 of 141
Found at i:3133711 original size:2 final size:2
Alignment explanation
Indices: 3133704--3133729 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3133694 TGTGGTGTTG
3133704 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
3133730 AACGTGCCAT
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):
TA
Found at i:3134857 original size:15 final size:16
Alignment explanation
Indices: 3134837--3134871 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
3134827 AAAAATTAAG
3134837 AAAAATGA-ATATTTT
1 AAAAATGAGATATTTT
*
3134852 AAAAATTAGATATTTT
1 AAAAATGAGATATTTT
3134868 AAAA
1 AAAA
3134872 TATTAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (16 bp):
AAAAATGAGATATTTT
Found at i:3134864 original size:16 final size:17
Alignment explanation
Indices: 3134845--3134876 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
3134835 AGAAAAATGA
3134845 ATATTTTAAAA-ATTAG
1 ATATTTTAAAATATTAG
3134861 ATATTTTAAAATATTA
1 ATATTTTAAAATATTA
3134877 ATTTTGAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATTTTAAAATATTAG
Found at i:3140342 original size:17 final size:17
Alignment explanation
Indices: 3140320--3140352 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3140310 TGTGATAAAT
3140320 TTTTAT-TTATTATATCA
1 TTTTATCTT-TTATATCA
3140337 TTTTATCTTTTATATC
1 TTTTATCTTTTATATC
3140353 TAGATTGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATCTTTTATATCA
Found at i:3146259 original size:11 final size:12
Alignment explanation
Indices: 3146231--3146259 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3146221 TTTAAAAAAA
3146231 ATAATATTTATG
1 ATAATATTTATG
3146243 ATAATATTTAT-
1 ATAATATTTATG
3146254 ATAATA
1 ATAATA
3146260 GGGGGTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (12 bp):
ATAATATTTATG
Found at i:3147242 original size:111 final size:110
Alignment explanation
Indices: 3147118--3147328 Score: 280
Period size: 111 Copynumber: 1.9 Consensus size: 110
3147108 AATAAATTTT
* * * ** * *
3147118 TTTTTAAAAATTAAGTAATTCATAAAACATGAAAGAGTTCTAA-AAGATTAGTTTACGGTAAATG
1 TTTTTAAAAATTAAGTAATTCATAAAACATGAAAAAATTCCAAGAA-AACAATTTACAGTAAATG
*
3147182 AAAGAATTACTTAAAATATGAAATAGTTACTTCAAACATAAAAATA
65 AAAAAATTACTTAAAATATGAAATAGTTACTTCAAACATAAAAATA
* * *
3147228 TTTTTAAAATATTAAGTAATTCGTAAAACATGAAAAAATTCCAAGAAAACAATTTATAGTACATG
1 TTTTTAAAA-ATTAAGTAATTCATAAAACATGAAAAAATTCCAAGAAAACAATTTACAGTAAATG
* *
3147293 AAAAAATTACTTAGAGTATGAAATAGTTACTTCAAA
65 AAAAAATTACTTAAAATATGAAATAGTTACTTCAAA
3147329 AGTGAAAAGA
Statistics
Matches: 86, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
110 9 0.10
111 75 0.87
112 2 0.02
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (110 bp):
TTTTTAAAAATTAAGTAATTCATAAAACATGAAAAAATTCCAAGAAAACAATTTACAGTAAATGA
AAAAATTACTTAAAATATGAAATAGTTACTTCAAACATAAAAATA
Found at i:3151478 original size:31 final size:30
Alignment explanation
Indices: 3151443--3151558 Score: 92
Period size: 31 Copynumber: 3.8 Consensus size: 30
3151433 TATTGTCCTG
*
3151443 GCAGACTATCTGTTATTTGTTTACAGTCCCA
1 GCAGACTATCTGTTATGTGTTTA-AGTCCCA
* * *
3151474 GCAGACCATTTGTTATGTGTTTAATGTCCTA
1 GCAGACTATCTGTTATGTGTTTAA-GTCCCA
* * *
3151505 G-TGAACTATCTGTTATGTGGTTATTGTCCCA
1 GCAG-ACTATCTGTTATGTGTTTA-AGTCCCA
* *
3151536 GTAGACTATTTG-TACTGTGTTTA
1 GCAGACTATCTGTTA-TGTGTTTA
3151559 CTATCTATGT
Statistics
Matches: 67, Mismatches: 13, Indels: 10
0.74 0.14 0.11
Matches are distributed among these distances:
30 4 0.06
31 62 0.93
32 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.20, T:0.42
Consensus pattern (30 bp):
GCAGACTATCTGTTATGTGTTTAAGTCCCA
Found at i:3160642 original size:12 final size:12
Alignment explanation
Indices: 3160625--3160652 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3160615 AGTTCAGGAG
3160625 ACACGATATGAA
1 ACACGATATGAA
3160637 ACACGATATGAA
1 ACACGATATGAA
3160649 ACAC
1 ACAC
3160653 AAAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.14, T:0.14
Consensus pattern (12 bp):
ACACGATATGAA
Found at i:3161502 original size:31 final size:31
Alignment explanation
Indices: 3161467--3161597 Score: 136
Period size: 31 Copynumber: 4.2 Consensus size: 31
3161457 ATCTTGATGG
3161467 ACTATCTGTTCTGTGTTTACTGTCCCAACAA
1 ACTATCTGTTCTGTGTTTACTGTCCCAACAA
* * ** *
3161498 ACTATCTGTTTTGTGTTTACTATCTTAGCAA
1 ACTATCTGTTCTGTGTTTACTGTCCCAACAA
* * * ** *
3161529 ACTATCTATTCTATGTTTATTGTCCCAGTAG
1 ACTATCTGTTCTGTGTTTACTGTCCCAACAA
* * *
3161560 ACTATTTGTTTTGTGTTTACTGTCCCAACGA
1 ACTATCTGTTCTGTGTTTACTGTCCCAACAA
3161591 ACTATCT
1 ACTATCT
3161598 CTGTGGGTGT
Statistics
Matches: 76, Mismatches: 24, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
31 76 1.00
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (31 bp):
ACTATCTGTTCTGTGTTTACTGTCCCAACAA
Found at i:3161594 original size:62 final size:62
Alignment explanation
Indices: 3161467--3161597 Score: 154
Period size: 62 Copynumber: 2.1 Consensus size: 62
3161457 ATCTTGATGG
* * ** *
3161467 ACTATCTGTTCTGTGTTTACTGTCCCAACAAACTATCTGTTTTGTGTTTACTATCTTAGCAA
1 ACTATCTATTCTATGTTTACTGTCCCAACAAACTATCTGTTTTGTGTTTACTATCCCAACAA
* ** * * * *
3161529 ACTATCTATTCTATGTTTATTGTCCCAGTAGACTATTTGTTTTGTGTTTACTGTCCCAACGA
1 ACTATCTATTCTATGTTTACTGTCCCAACAAACTATCTGTTTTGTGTTTACTATCCCAACAA
3161591 ACTATCT
1 ACTATCT
3161598 CTGTGGGTGT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.22, C:0.21, G:0.13, T:0.44
Consensus pattern (62 bp):
ACTATCTATTCTATGTTTACTGTCCCAACAAACTATCTGTTTTGTGTTTACTATCCCAACAA
Found at i:3165059 original size:31 final size:31
Alignment explanation
Indices: 3165010--3165276 Score: 344
Period size: 31 Copynumber: 8.7 Consensus size: 31
3165000 GTATATGTTT
* * *
3165010 TATACATTACTGAA-TTGATTTGTATAAAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
3165040 TATACATTACCGAATTTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * * *
3165071 TATACATTGCCAAATTTAATCTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
3165102 TATACATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
3165132 TATACATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
3165163 TATACATTGCCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
3165194 TATTCATTGTCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
3165224 TATATATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
3165255 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
3165277 ACCATTGGAT
Statistics
Matches: 211, Mismatches: 23, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
30 73 0.35
31 138 0.65
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.43
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATAGA
Found at i:3165130 original size:61 final size:62
Alignment explanation
Indices: 3165010--3165276 Score: 344
Period size: 61 Copynumber: 4.4 Consensus size: 62
3165000 GTATATGTTT
* * * * *
3165010 TATACATTACTGAA-TTGATTTGTATAAAGATATACATTACCGAATTTGATTTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * *
3165071 TATACATTGCCAAATTTAATCTGTTTATAGATATACATTGCCGAA-TTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * *
3165132 TATACATTGCCGAATTTGATTTGTATATGGTTATACATTGCCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
* * * * *
3165194 TATTCATTGTCGAA-TTGATTTGTATATAGATATATATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
*
3165255 TATATATTGCCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
3165277 ACCATTGGAT
Statistics
Matches: 179, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
61 127 0.71
62 52 0.29
ACGTcount: A:0.31, C:0.09, G:0.16, T:0.43
Consensus pattern (62 bp):
TATACATTGCCGAATTTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATAGA
Found at i:3165148 original size:92 final size:92
Alignment explanation
Indices: 3165010--3165270 Score: 369
Period size: 92 Copynumber: 2.8 Consensus size: 92
3165000 GTATATGTTT
* * * * * *
3165010 TATACATTACTGAATTGATTTGTATAAAGATATACATTACCGAATTTGATTTGTTTATAGATATA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATA
* *
3165075 CATTGCCAAATTTAATCTGTTTATAGA
66 CATTGCCGAATTTAATCTGTATATAGA
*
3165102 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGTTATA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATA
* * *
3165167 CATTGCCGAATTTGATTTGTATATGGA
66 CATTGCCGAATTTAATCTGTATATAGA
* * * *
3165194 TATTCATTGTCGAATTGATTTGTATATAGATATATATTGCCGAATTTGATTCGTATATGGATATA
1 TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATA
*
3165259 TATTGCCGAATT
66 CATTGCCGAATT
3165271 GATTTGACCA
Statistics
Matches: 151, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
92 151 1.00
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.43
Consensus pattern (92 bp):
TATACATTGCCGAATTGATTTGTATATAGATATACATTGCCGAATTTGATTTGTATATGGATATA
CATTGCCGAATTTAATCTGTATATAGA
Found at i:3172129 original size:31 final size:29
Alignment explanation
Indices: 3172105--3172493 Score: 323
Period size: 31 Copynumber: 12.8 Consensus size: 29
3172095 GTATATGTTT
**
3172105 TATACATTGCCGAATTGATTTGTATAAAAA
1 TATACATTGCCGAATTGATTTGTAT-ATGA
* *
3172135 TATACATTGTCGAATTTGATTTGTTTATAGA
1 TATACATTGCCGAA-TTGATTTGTATAT-GA
* * *
3172166 TATACATTGCCAAATTTGATCTGTTTATAGA
1 TATACATTGCCGAA-TTGATTTGTATAT-GA
** *
3172197 TATACATTGCCGAAATTGATCAGTTTATAGA
1 TATACATTGCCG-AATTGATTTGTATAT-GA
3172228 TATACATTGCCGAATTGATTTGTATATAGA
1 TATACATTGCCGAATTGATTTGTATAT-GA
* * * *
3172258 AATAAATTGCCGAATTTGATTTGTTTATGGT
1 TATACATTGCCGAA-TTGATTTGTATAT-GA
* * *
3172289 TATACATTGTCGGATTTAAATTT-TATATGGA
1 TATACATTG-CCGAATT-GATTTGTATAT-GA
*
3172320 TATAAATTGCCGAATTGA-TTGTATATAGA
1 TATACATTGCCGAATTGATTTGTATAT-GA
* * *
3172349 TATACGTTGCTGAATTTGATTTGTATATGGT
1 TATACATTGCCGAA-TTGATTTGTATAT-GA
*
3172380 TATACATTGCTGAATTTGATTTGTATATGGA
1 TATACATTGCCGAA-TTGATTTGTATAT-GA
* *
3172411 TATTCATTGCCAAATTGATTTGTATATAGA
1 TATACATTGCCGAATTGATTTGTATAT-GA
* *
3172441 TATAAATTGCCGAATTTGATTCGTATATGGA
1 TATACATTGCCGAA-TTGATTTGTATAT-GA
* *
3172472 TATATATTGCTGAATTGATTTG
1 TATACATTGCCGAATTGATTTG
3172494 AGCATTGGAT
Statistics
Matches: 301, Mismatches: 48, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.01
29 19 0.06
30 83 0.28
31 188 0.62
32 9 0.03
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (29 bp):
TATACATTGCCGAATTGATTTGTATATGA
Found at i:3172246 original size:92 final size:91
Alignment explanation
Indices: 3172105--3172491 Score: 418
Period size: 92 Copynumber: 4.2 Consensus size: 91
3172095 GTATATGTTT
* * * * *
3172105 TATACATTGCCGAATTGATTTGTATAAAAATATACATTGTCGAATTTGATTTGTTTATAGATATA
1 TATACATTGCCGAATTGATTAGTATATAGATATACATTGCCGAA-TTGATTTGTATATAGATATA
* * * * *
3172170 CATTGCCAAATTTGATCTGTTTATAGA
65 AATTGCCGAATTTGATTTGTATATGGA
* * *
3172197 TATACATTGCCGAAATTGATCAGTTTATAGATATACATTGCCGAATTGATTTGTATATAGAAATA
1 TATACATTGCCG-AATTGATTAGTATATAGATATACATTGCCGAATTGATTTGTATATAGATATA
* *
3172262 AATTGCCGAATTTGATTTGTTTATGGT
65 AATTGCCGAATTTGATTTGTATATGGA
* * * * * *
3172289 TATACATTGTCGGATTTAAATT-TTATATGGATATAAATTGCCGAATTGA-TTGTATATAGATAT
1 TATACATTG-CCGAATT-GATTAGTATATAGATATACATTGCCGAATTGATTTGTATATAGATAT
** * *
3172352 ACGTTGCTGAATTTGATTTGTATATGGT
64 AAATTGCCGAATTTGATTTGTATATGGA
* * * * *
3172380 TATACATTGCTGAATTTGATTTGTATATGGATATTCATTGCCAAATTGATTTGTATATAGATATA
1 TATACATTGCCGAA-TTGATTAGTATATAGATATACATTGCCGAATTGATTTGTATATAGATATA
*
3172445 AATTGCCGAATTTGATTCGTATATGGA
65 AATTGCCGAATTTGATTTGTATATGGA
* *
3172472 TATATATTGCTGAATTGATT
1 TATACATTGCCGAATTGATT
3172492 TGAGCATTGG
Statistics
Matches: 250, Mismatches: 39, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
90 6 0.02
91 77 0.31
92 137 0.55
93 30 0.12
ACGTcount: A:0.32, C:0.09, G:0.17, T:0.43
Consensus pattern (91 bp):
TATACATTGCCGAATTGATTAGTATATAGATATACATTGCCGAATTGATTTGTATATAGATATAA
ATTGCCGAATTTGATTTGTATATGGA
Found at i:3183148 original size:19 final size:19
Alignment explanation
Indices: 3183124--3183172 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
3183114 ATGCTTATGC
3183124 TTGAGTTTGAGTCTTGGTG
1 TTGAGTTTGAGTCTTGGTG
3183143 TTGAGTTTGAGTCTTGGTG
1 TTGAGTTTGAGTCTTGGTG
*
3183162 TTTAGTTTGAG
1 TTGAGTTTGAG
3183173 CTATTTTGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.12, C:0.04, G:0.35, T:0.49
Consensus pattern (19 bp):
TTGAGTTTGAGTCTTGGTG
Found at i:3187251 original size:31 final size:31
Alignment explanation
Indices: 3187212--3187287 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
3187202 CTGTTTTGTA
* *
3187212 TTTACTGTCCAAGCAGACAATTTATTCTGTG
1 TTTACTGTCCAAGCAGACAATCTATTATGTG
* * *
3187243 TTTGCTGTCCCAGCAGACTATCTATTATGTG
1 TTTACTGTCCAAGCAGACAATCTATTATGTG
*
3187274 TTTACTATCCAAGC
1 TTTACTGTCCAAGC
3187288 GAACTATCTC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.38
Consensus pattern (31 bp):
TTTACTGTCCAAGCAGACAATCTATTATGTG
Found at i:3190107 original size:25 final size:25
Alignment explanation
Indices: 3190079--3190127 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
3190069 GTTTTCATAC
*
3190079 TTTGAATACAAGATATTTTAGTATG
1 TTTGAATACAAGAAATTTTAGTATG
3190104 TTTGAATACAAGAAATTTTAGTAT
1 TTTGAATACAAGAAATTTTAGTAT
3190128 ATTTTAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (25 bp):
TTTGAATACAAGAAATTTTAGTATG
Found at i:3193951 original size:30 final size:30
Alignment explanation
Indices: 3193917--3194140 Score: 272
Period size: 30 Copynumber: 7.5 Consensus size: 30
3193907 TCATCGACTA
* * *
3193917 ATGAAAAGGGATGG-TGACAACCATCGAATT
1 ATGAAAAGGGATGGCT-TCGACTATCGAATT
* *
3193947 ATGAAAATGGATGGCTTCGACTATCAAATT
1 ATGAAAAGGGATGGCTTCGACTATCGAATT
3193977 ATGAAAAGGGATGGCTTC-AGCTATCGAATT
1 ATGAAAAGGGATGGCTTCGA-CTATCGAATT
* *
3194007 ATGAAAAGGGATGGCTTCGGCTATCGATTT
1 ATGAAAAGGGATGGCTTCGACTATCGAATT
* * *
3194037 ATGAAAATGGATGGCTTCGGCTATTGAATT
1 ATGAAAAGGGATGGCTTCGACTATCGAATT
* *
3194067 ATGAAAGGGGATGGCTTCGGCTATCGAATT
1 ATGAAAAGGGATGGCTTCGACTATCGAATT
* * *
3194097 ATGTAAAGGGATGGCTTCAACTATCAAATT
1 ATGAAAAGGGATGGCTTCGACTATCGAATT
*
3194127 ATGGAAAGGGATGG
1 ATGAAAAGGGATGG
3194141 TGACGACCAT
Statistics
Matches: 170, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
29 1 0.01
30 168 0.99
31 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.28, T:0.27
Consensus pattern (30 bp):
ATGAAAAGGGATGGCTTCGACTATCGAATT
Found at i:3194153 original size:30 final size:29
Alignment explanation
Indices: 3194093--3194180 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
3194083 TCGGCTATCG
* * *
3194093 AATTATGTAAAGGGATGGCTTCAACTATCA
1 AATTATGGAAAGGGATGG-TACAACCATCA
*
3194123 AATTATGGAAAGGGATGGTGACGACCATCA
1 AATTATGGAAAGGGATGGT-ACAACCATCA
*
3194153 ACA--ATGGAAAGGGTTGGTAACAACCATC
1 A-ATTATGGAAAGGGATGGT-ACAACCATC
3194181 GTGATTTTAC
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
29 23 0.47
30 25 0.51
31 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (29 bp):
AATTATGGAAAGGGATGGTACAACCATCA
Found at i:3194163 original size:90 final size:90
Alignment explanation
Indices: 3193917--3194165 Score: 229
Period size: 90 Copynumber: 2.8 Consensus size: 90
3193907 TCATCGACTA
* * * * * *
3193917 ATGAAAAGGGATGG-TGACAACCATCGAATTATGAAAATGGATGGCTTCGACTA-TCAA-ATTAT
1 ATGAAAAGGGATGGCT-TCAACTATCAAATTATGAAAAGGGATGGCTACGACCATTCAACA--AT
*
3193979 GAAAAGGGATGGCTTCAGCTATCGAATT
63 GAAAGGGGATGGCTTCAGCTATCGAATT
** * * * * * * * **
3194007 ATGAAAAGGGATGGCTTCGGCTATCGATTTATGAAAATGGATGGCTTCGGCTATTGAATTATGAA
1 ATGAAAAGGGATGGCTTCAACTATCAAATTATGAAAAGGGATGGCTACGACCATTCAACAATGAA
*
3194072 AGGGGATGGCTTCGGCTATCGAATT
66 AGGGGATGGCTTCAGCTATCGAATT
* *
3194097 ATGTAAAGGGATGGCTTCAACTATCAAATTATGGAAAGGGATGG-TGACGACCA-TCAACAATGG
1 ATGAAAAGGGATGGCTTCAACTATCAAATTATGAAAAGGGATGGCT-ACGACCATTCAACAAT-G
3194160 AAAGGG
64 AAAGGG
3194166 TTGGTAACAA
Statistics
Matches: 131, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
89 6 0.05
90 121 0.92
91 4 0.03
ACGTcount: A:0.34, C:0.13, G:0.28, T:0.26
Consensus pattern (90 bp):
ATGAAAAGGGATGGCTTCAACTATCAAATTATGAAAAGGGATGGCTACGACCATTCAACAATGAA
AGGGGATGGCTTCAGCTATCGAATT
Found at i:3202268 original size:17 final size:17
Alignment explanation
Indices: 3202246--3202287 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 17
3202236 GTGTGATGTA
3202246 TGAAAAAGATCA-AAAAG
1 TGAAAAAG-TCACAAAAG
3202263 TGAAAAAGTCACAAAAG
1 TGAAAAAGTCACAAAAG
3202280 TAGAAAAA
1 T-GAAAAA
3202288 CTTAGTCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.13
17 14 0.61
18 6 0.26
ACGTcount: A:0.64, C:0.07, G:0.17, T:0.12
Consensus pattern (17 bp):
TGAAAAAGTCACAAAAG
Found at i:3229042 original size:22 final size:23
Alignment explanation
Indices: 3228979--3229044 Score: 73
Period size: 22 Copynumber: 2.9 Consensus size: 23
3228969 CTAGCAAAAT
* *
3228979 GCCACAAAGGCTAAT-AGAATAT
1 GCCACAAAGGCAAATCAGAATAC
*
3229001 GCCACAAAGGCCAAATCAGAGTAC
1 GCCACAAAGG-CAAATCAGAATAC
*
3229025 GCCATAAAGGC-AATCAGAAT
1 GCCACAAAGGCAAATCAGAAT
3229045 GCCACCCAGA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 18 0.49
23 5 0.14
24 14 0.38
ACGTcount: A:0.44, C:0.23, G:0.20, T:0.14
Consensus pattern (23 bp):
GCCACAAAGGCAAATCAGAATAC
Found at i:3233706 original size:17 final size:18
Alignment explanation
Indices: 3233666--3233706 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
3233656 TGACACTTCA
*
3233666 TCTTTTTATTCTTATTTT
1 TCTTTTTATTCTCATTTT
*
3233684 T-ATTTTATT-TCATTTT
1 TCTTTTTATTCTCATTTT
3233700 TCTTTTT
1 TCTTTTT
3233707 GTAGAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 3
0.76 0.12 0.12
Matches are distributed among these distances:
16 7 0.37
17 11 0.58
18 1 0.05
ACGTcount: A:0.12, C:0.10, G:0.00, T:0.78
Consensus pattern (18 bp):
TCTTTTTATTCTCATTTT
Found at i:3238817 original size:27 final size:27
Alignment explanation
Indices: 3238764--3238818 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
3238754 TAAAGTATCA
* **
3238764 AAAGGTTAAAAATGTAAATAGGTAAAT
1 AAAGGTTAAAAATGTAAAAAGCAAAAT
3238791 AAAGGTTAAAAAT-TAAAGAAGCAAAAT
1 AAAGGTTAAAAATGTAAA-AAGCAAAAT
3238818 A
1 A
3238819 TGCTATCATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 4 0.17
27 20 0.83
ACGTcount: A:0.60, C:0.02, G:0.16, T:0.22
Consensus pattern (27 bp):
AAAGGTTAAAAATGTAAAAAGCAAAAT
Found at i:3239624 original size:25 final size:24
Alignment explanation
Indices: 3239596--3239746 Score: 94
Period size: 25 Copynumber: 6.1 Consensus size: 24
3239586 CATTAAGGAT
*
3239596 TACCGATTCTCAGCTCATATGAGCA
1 TACCGATTCTCAGCTCGTA-GAGCA
* * *
3239621 TACCAATT-GCAGCTCGTGAGAGCT
1 TACCGATTCTCAGCTCGT-AGAGCA
* *
3239645 TACCGATTGT-AGCTCGTGAGAGCT
1 TACCGATTCTCAGCTCGT-AGAGCA
* *
3239669 TAGCGATTCTCAGCTCGTATGAGCT
1 TACCGATTCTCAGCTCGTA-GAGCA
** *
3239694 TACTAATT-TCCAGCTCGAGAGAGCA
1 TACCGATTCT-CAGCTCG-TAGAGCA
*
3239719 TAGCGATTCAT-AGCTCGTATGAGCA
1 TACCGATTC-TCAGCTCGTA-GAGCA
3239744 TAC
1 TAC
3239747 ATGAACAAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 18
0.73 0.13 0.13
Matches are distributed among these distances:
24 43 0.43
25 54 0.55
26 1 0.01
27 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.28
Consensus pattern (24 bp):
TACCGATTCTCAGCTCGTAGAGCA
Found at i:3239643 original size:24 final size:24
Alignment explanation
Indices: 3239616--3239717 Score: 89
Period size: 24 Copynumber: 4.2 Consensus size: 24
3239606 CAGCTCATAT
*
3239616 GAGCATACCAATTGCAGCTCGTGA
1 GAGCTTACCAATTGCAGCTCGTGA
* *
3239640 GAGCTTACCGATTGTAGCTCGTGA
1 GAGCTTACCAATTGCAGCTCGTGA
* * *
3239664 GAGCTTAGCGATTCTCAGCTCGT-A
1 GAGCTTACCAATT-GCAGCTCGTGA
* * *
3239688 TGAGCTTACTAATTTCCAGCTCGAGA
1 -GAGCTTACCAA-TTGCAGCTCGTGA
3239714 GAGC
1 GAGC
3239718 ATAGCGATTC
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
24 34 0.54
25 26 0.41
26 3 0.05
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (24 bp):
GAGCTTACCAATTGCAGCTCGTGA
Found at i:3260648 original size:40 final size:41
Alignment explanation
Indices: 3260604--3260691 Score: 133
Period size: 40 Copynumber: 2.2 Consensus size: 41
3260594 AATTCATTAC
* *
3260604 TTCAGTAATTTCACAATTCAATGCAGTACAC-ATAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAAACAATA
* *
3260644 TTCAGTAACTTCACAATTCAATTCAGTACTCAAAAACAATA
1 TTCAGTAACTTCACAATTCAATGCAGTACACAAAAACAATA
3260685 TTCAGTA
1 TTCAGTA
3260692 TTCCATAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
40 28 0.65
41 15 0.35
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (41 bp):
TTCAGTAACTTCACAATTCAATGCAGTACACAAAAACAATA
Found at i:3260669 original size:21 final size:21
Alignment explanation
Indices: 3260604--3260671 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
3260594 AATTCATTAC
*
3260604 TTCAGTAATTTCACAATTCAA
1 TTCAGTAACTTCACAATTCAA
* * *
3260625 TGCAGTACACATAACAA-T--A
1 TTCAGTA-ACTTCACAATTCAA
3260644 TTCAGTAACTTCACAATTCAA
1 TTCAGTAACTTCACAATTCAA
3260665 TTCAGTA
1 TTCAGTA
3260672 CTCAAAAACA
Statistics
Matches: 36, Mismatches: 7, Indels: 8
0.71 0.14 0.16
Matches are distributed among these distances:
18 7 0.19
19 8 0.22
21 15 0.42
22 6 0.17
ACGTcount: A:0.40, C:0.21, G:0.07, T:0.32
Consensus pattern (21 bp):
TTCAGTAACTTCACAATTCAA
Found at i:3260947 original size:26 final size:25
Alignment explanation
Indices: 3260916--3260965 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
3260906 TAGTTCAATA
3260916 ATTCAATTCAAAC-CATTTCAATTTCT
1 ATTCAA-T-AAACACATTTCAATTTCT
*
3260942 ATTCAATAATCACATTTCAATTTC
1 ATTCAATAAACACATTTCAATTTC
3260966 ACTTTCTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 3 0.14
25 13 0.59
26 6 0.27
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTCAATAAACACATTTCAATTTCT
Found at i:3272177 original size:14 final size:14
Alignment explanation
Indices: 3272158--3272189 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
3272148 TTTCATATCC
3272158 ATAACACACCAGTT
1 ATAACACACCAGTT
3272172 ATAACACACCAGTT
1 ATAACACACCAGTT
3272186 ATAA
1 ATAA
3272190 GCATATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.25, G:0.06, T:0.22
Consensus pattern (14 bp):
ATAACACACCAGTT
Found at i:3272768 original size:42 final size:42
Alignment explanation
Indices: 3272706--3272828 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 42
3272696 AAGCTCATGG
**
3272706 GAGCTAAACAAAAACCCATAAGGGTTGAACGGAAGCTCGTAA-A
1 GAGCTAAACGGAAACCCATAAGGGTTGAACGGAAGCTC--AATA
* ** * * **
3272749 -AGCTGAACGGAAATTCATAAAGGTTAAACAAAAGCTCAATA
1 GAGCTAAACGGAAACCCATAAGGGTTGAACGGAAGCTCAATA
* *
3272790 GAGCTAAACGGAAACCCATTAGGGTTGAACGGAAACTCA
1 GAGCTAAACGGAAACCCATAAGGGTTGAACGGAAGCTCA
3272829 TATGAGTTAA
Statistics
Matches: 60, Mismatches: 18, Indels: 5
0.72 0.22 0.06
Matches are distributed among these distances:
40 2 0.03
41 1 0.02
42 57 0.95
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (42 bp):
GAGCTAAACGGAAACCCATAAGGGTTGAACGGAAGCTCAATA
Found at i:3285156 original size:27 final size:27
Alignment explanation
Indices: 3285109--3285212 Score: 122
Period size: 27 Copynumber: 3.8 Consensus size: 27
3285099 AAACATGCCA
* *
3285109 GAAAAAGGAAG-CTTTTGTGGCTATCAAT
1 GAAAAA-GAAGTC-TTTGTGGCGATCTAT
*
3285137 GAAAAAGAAGTCTTTCTGGCGATCTAT
1 GAAAAAGAAGTCTTTGTGGCGATCTAT
3285164 GAAAATAG-AGTCTTTGTGGCGATCTAT
1 GAAAA-AGAAGTCTTTGTGGCGATCTAT
* *
3285191 GAAAAGGAAGCCTTTGTGGCGA
1 GAAAAAGAAGTCTTTGTGGCGA
3285213 ACTCTAAAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 7
0.84 0.08 0.09
Matches are distributed among these distances:
26 1 0.01
27 57 0.85
28 9 0.13
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (27 bp):
GAAAAAGAAGTCTTTGTGGCGATCTAT
Found at i:3286420 original size:12 final size:12
Alignment explanation
Indices: 3286400--3286433 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
3286390 GGGGACACAC
*
3286400 GCCCGTGTCCTA
1 GCCCATGTCCTA
3286412 GCCCATGTCCTA
1 GCCCATGTCCTA
3286424 GCCCATGTCC
1 GCCCATGTCC
3286434 AAACTAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.12, C:0.44, G:0.21, T:0.24
Consensus pattern (12 bp):
GCCCATGTCCTA
Found at i:3293952 original size:24 final size:24
Alignment explanation
Indices: 3293925--3293972 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3293915 CTTATTTAAC
*
3293925 AATTCAAAT-ATTATTATAATAAAA
1 AATTCAAATCATAATTA-AATAAAA
3293949 AATTCAAATCATAATTAAATAAAA
1 AATTCAAATCATAATTAAATAAAA
3293973 TTTACTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
AATTCAAATCATAATTAAATAAAA
Found at i:3297724 original size:3 final size:3
Alignment explanation
Indices: 3297718--3297746 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3297708 CTACTACTAC
3297718 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
3297747 ACTAGATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3297873 original size:18 final size:18
Alignment explanation
Indices: 3297850--3297884 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3297840 TCTTAAGATA
3297850 ATAATTATAATTATAAGT
1 ATAATTATAATTATAAGT
* *
3297868 ATAATTCTAATTTTAAG
1 ATAATTATAATTATAAG
3297885 AAAATATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.46
Consensus pattern (18 bp):
ATAATTATAATTATAAGT
Found at i:3297893 original size:22 final size:22
Alignment explanation
Indices: 3297867--3297912 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
3297857 TAATTATAAG
3297867 TATAATTCTAATTTTAAGAAAA
1 TATAATTCTAATTTTAAGAAAA
3297889 TATAATTCTAATTTTAAGAAAA
1 TATAATTCTAATTTTAAGAAAA
3297911 TA
1 TA
3297913 GTTTGTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (22 bp):
TATAATTCTAATTTTAAGAAAA
Found at i:3298658 original size:54 final size:53
Alignment explanation
Indices: 3298576--3298681 Score: 158
Period size: 54 Copynumber: 2.0 Consensus size: 53
3298566 GTTAATGCCT
* *
3298576 TAAAAGAAGTAAATCGAATTCATAAGTCTATGATTATCTTCCTTATGGAAACCC
1 TAAAAGAACTAAATCGAATTAATAAGTCTATGATTATC-TCCTTATGGAAACCC
** *
3298630 TAAAAGAACTAAATTTAATTAATAAGTCTATGATTATCTCTTTATGGAAACC
1 TAAAAGAACTAAATCGAATTAATAAGTCTATGATTATCTCCTTATGGAAACC
3298682 AAAATGAAGA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
53 13 0.28
54 34 0.72
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (53 bp):
TAAAAGAACTAAATCGAATTAATAAGTCTATGATTATCTCCTTATGGAAACCC
Found at i:3300683 original size:33 final size:34
Alignment explanation
Indices: 3300593--3300688 Score: 106
Period size: 34 Copynumber: 2.9 Consensus size: 34
3300583 GGACTCTATC
*
3300593 TGTGTTTACTGTCTCAGCGGACTATCT-TTGTTT
1 TGTGTTTACTGTCCCAGCGGACTATCTCTTGTTT
** *
3300626 TGTGTTTTTTTATCCCAGCGGACTATCTCTT-TTT
1 TGTG-TTTACTGTCCCAGCGGACTATCTCTTGTTT
* * *
3300660 TGTGTTTAGTGTCCCAACAGACTATCTCT
1 TGTGTTTACTGTCCCAGCGGACTATCTCT
3300689 ATGGATTCCA
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
33 24 0.46
34 26 0.50
35 2 0.04
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (34 bp):
TGTGTTTACTGTCCCAGCGGACTATCTCTTGTTT
Found at i:3306446 original size:14 final size:14
Alignment explanation
Indices: 3306427--3306455 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
3306417 AAAACAGATT
3306427 TAACTATACTAAAA
1 TAACTATACTAAAA
3306441 TAACTATACTAAAA
1 TAACTATACTAAAA
3306455 T
1 T
3306456 GATCATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (14 bp):
TAACTATACTAAAA
Found at i:3309707 original size:14 final size:14
Alignment explanation
Indices: 3309688--3309715 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3309678 TAAAGTTATA
3309688 TTTAATAATTCATT
1 TTTAATAATTCATT
3309702 TTTAATAATTCATT
1 TTTAATAATTCATT
3309716 AATAAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:3316926 original size:18 final size:18
Alignment explanation
Indices: 3316903--3316938 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
3316893 AGAAGTGAAA
3316903 GAGCGATTTAATTAAATT
1 GAGCGATTTAATTAAATT
3316921 GAGCGATTTAATTAAATT
1 GAGCGATTTAATTAAATT
3316939 TTCAAGCATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.06, G:0.17, T:0.39
Consensus pattern (18 bp):
GAGCGATTTAATTAAATT
Found at i:3323237 original size:91 final size:91
Alignment explanation
Indices: 3323082--3323264 Score: 366
Period size: 91 Copynumber: 2.0 Consensus size: 91
3323072 ACCACTATGA
3323082 CACCTCCTTTCTTAGGTACACATTGTACAGGACTCACCCATGAGCTGTCTGAAATCGGGTAAATG
1 CACCTCCTTTCTTAGGTACACATTGTACAGGACTCACCCATGAGCTGTCTGAAATCGGGTAAATG
3323147 ATGCTAGCATCAAGCCACTTAATAAT
66 ATGCTAGCATCAAGCCACTTAATAAT
3323173 CACCTCCTTTCTTAGGTACACATTGTACAGGACTCACCCATGAGCTGTCTGAAATCGGGTAAATG
1 CACCTCCTTTCTTAGGTACACATTGTACAGGACTCACCCATGAGCTGTCTGAAATCGGGTAAATG
3323238 ATGCTAGCATCAAGCCACTTAATAAT
66 ATGCTAGCATCAAGCCACTTAATAAT
3323264 C
1 C
3323265 TCTTTCTTGA
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 92 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (91 bp):
CACCTCCTTTCTTAGGTACACATTGTACAGGACTCACCCATGAGCTGTCTGAAATCGGGTAAATG
ATGCTAGCATCAAGCCACTTAATAAT
Found at i:3332827 original size:16 final size:17
Alignment explanation
Indices: 3332802--3332834 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
3332792 ATTTTTCACG
*
3332802 TTATTAATAAATCATTC
1 TTATTAATAAAGCATTC
3332819 TTATT-ATAAAGCATTC
1 TTATTAATAAAGCATTC
3332835 GCTTGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.39, C:0.12, G:0.03, T:0.45
Consensus pattern (17 bp):
TTATTAATAAAGCATTC
Found at i:3335550 original size:47 final size:48
Alignment explanation
Indices: 3335477--3335571 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 48
3335467 AATGTTGTAA
3335477 TTCTTTAACGAAACTTTAAGAAATGTTTAGAAACCTTCTAATCATGTC
1 TTCTTTAACGAAACTTTAAGAAATGTTTAGAAACCTTCTAATCATGTC
3335525 TTCTTTAACGAAA-TTTAAGAAATGTTTAGAAACCTTCTAATCATGTC
1 TTCTTTAACGAAACTTTAAGAAATGTTTAGAAACCTTCTAATCATGTC
3335572 AAAACTAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 34 0.72
48 13 0.28
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.38
Consensus pattern (48 bp):
TTCTTTAACGAAACTTTAAGAAATGTTTAGAAACCTTCTAATCATGTC
Found at i:3337567 original size:57 final size:58
Alignment explanation
Indices: 3337503--3337616 Score: 151
Period size: 59 Copynumber: 2.0 Consensus size: 58
3337493 ATCACTTTAA
*
3337503 TATTAAATAAATATAATAC-TTAT-TAAGATAAATATTAGATTAAATTTAATATTAATC
1 TATTAAATAAATAGAATACTTTATATAAGATAAATATTA-ATTAAATTTAATATTAATC
* * * *
3337560 TATTAAATTAATAGAATACTTTTCTATAAGATGAATATTAATTTAATTTAATATTAA
1 TATTAAATAAATAGAATAC-TTTATATAAGATAAATATTAATTAAATTTAATATTAA
3337617 GATAATCACT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 17 0.35
59 19 0.39
60 13 0.27
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (58 bp):
TATTAAATAAATAGAATACTTTATATAAGATAAATATTAATTAAATTTAATATTAATC
Found at i:3339548 original size:29 final size:30
Alignment explanation
Indices: 3339507--3339563 Score: 107
Period size: 29 Copynumber: 1.9 Consensus size: 30
3339497 ACTTGGTTGT
3339507 GATATCTAAAGTAATAAACACTTAATCATG
1 GATATCTAAAGTAATAAACACTTAATCATG
3339537 GATATCT-AAGTAATAAACACTTAATCA
1 GATATCTAAAGTAATAAACACTTAATCA
3339564 AAATTGTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.47, C:0.14, G:0.09, T:0.30
Consensus pattern (30 bp):
GATATCTAAAGTAATAAACACTTAATCATG
Found at i:3344776 original size:25 final size:25
Alignment explanation
Indices: 3344745--3344802 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
3344735 GCTATAAACG
*
3344745 GTAAGCTCGTCTGAGCTAAATAACA
1 GTAAGCTCCTCTGAGCTAAATAACA
* * *
3344770 GTAAGCTCCTCTGATCTGAATAACG
1 GTAAGCTCCTCTGAGCTAAATAACA
3344795 GTAAGCTC
1 GTAAGCTC
3344803 ATGCGAGCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (25 bp):
GTAAGCTCCTCTGAGCTAAATAACA
Found at i:3344839 original size:50 final size:50
Alignment explanation
Indices: 3344725--3344847 Score: 112
Period size: 50 Copynumber: 2.5 Consensus size: 50
3344715 GAATCAGTAT
* * *
3344725 GCTCTTACGAGCT--ATAAACGGTAAGCTCGTCTGAGCTAAATAACAGTAA
1 GCTCATACGAGCTGAAT-AACGGTAAGCTCATCTGAGCTAAATAACAATAA
* * * *
3344774 GCTCCT-CTGATCTGAATAACGGTAAGCTCATGC-GAGCTAAGTATCAATAA
1 GCTCATAC-GAGCTGAATAACGGTAAGCTCAT-CTGAGCTAAATAACAATAA
*
3344824 GCTCATACGAGCTGAA-ATCGGTAA
1 GCTCATACGAGCTGAATAACGGTAA
3344848 CCCTAATGAC
Statistics
Matches: 60, Mismatches: 9, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
48 1 0.02
49 16 0.27
50 39 0.65
51 4 0.07
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (50 bp):
GCTCATACGAGCTGAATAACGGTAAGCTCATCTGAGCTAAATAACAATAA
Found at i:3345807 original size:23 final size:23
Alignment explanation
Indices: 3345777--3345821 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
3345767 ATAGTAGGTT
3345777 CTTAAATTATTGTGATTAAAATC
1 CTTAAATTATTGTGATTAAAATC
*
3345800 CTTAAATTATTGTGGTTAAAAT
1 CTTAAATTATTGTGATTAAAAT
3345822 ATGATACTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.07, G:0.11, T:0.44
Consensus pattern (23 bp):
CTTAAATTATTGTGATTAAAATC
Found at i:3346218 original size:27 final size:27
Alignment explanation
Indices: 3346194--3346487 Score: 374
Period size: 27 Copynumber: 10.9 Consensus size: 27
3346184 GTTATGACTA
*
3346194 AAATACCCCCATAGGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
3346221 AAATACCCCCATAAGATAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
3346248 AAATACCCCCATAAGATAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
3346275 AAATACCCCTATAGGGTAAAATTACCA
1 AAATACCCCCATAGGGTAAAATGACCG
*
3346302 AAATACCCCCACAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
3346329 AAATACCACTATAGGGTAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
** *
3346356 AAATACCCTTATAGGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
** * * *
3346383 AAATACATCTATATGGTAAAATGACCA
1 AAATACCCCCATAGGGTAAAATGACCG
*
3346410 AAATACCCCCATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
3346437 AAATACCCCC-TAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
3346463 AAATACCCTCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
3346488 TTTTATACCC
Statistics
Matches: 230, Mismatches: 36, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
26 24 0.10
27 206 0.90
ACGTcount: A:0.43, C:0.22, G:0.16, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGACCG
Found at i:3346662 original size:26 final size:26
Alignment explanation
Indices: 3346626--3346732 Score: 151
Period size: 26 Copynumber: 4.1 Consensus size: 26
3346616 TGGAGGAAGT
* *
3346626 ATACTGATACTGGCAGCTTTGCTGCG
1 ATACTGTTACTGGCAGCTTTGCTACG
*
3346652 ATACTGTTACTGTCAGCTTTGCTACG
1 ATACTGTTACTGGCAGCTTTGCTACG
*
3346678 ATATTGTTACTGGCAGCTTTGCTACG
1 ATACTGTTACTGGCAGCTTTGCTACG
* * *
3346704 ATACTATTTCTGGAAGCTTTGCTACG
1 ATACTGTTACTGGCAGCTTTGCTACG
3346730 ATA
1 ATA
3346733 TTAGTGTGTT
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 72 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (26 bp):
ATACTGTTACTGGCAGCTTTGCTACG
Found at i:3346866 original size:33 final size:33
Alignment explanation
Indices: 3346829--3346905 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 33
3346819 TGCATTATTG
* * *
3346829 CACTGTACTGATACTGTATTGGGCTAAGGCCCA
1 CACTGTACTGATACTGAATAGCGCTAAGGCCCA
* *
3346862 CACTGTACTGTTACTGAATAGCGCTCAGGCCCA
1 CACTGTACTGATACTGAATAGCGCTAAGGCCCA
*
3346895 GACTGTTACTG
1 CACTG-TACTG
3346906 CATGTTGTAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 32 0.86
34 5 0.14
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.27
Consensus pattern (33 bp):
CACTGTACTGATACTGAATAGCGCTAAGGCCCA
Found at i:3355818 original size:196 final size:196
Alignment explanation
Indices: 3355484--3355872 Score: 724
Period size: 196 Copynumber: 2.0 Consensus size: 196
3355474 ACTAAATTTT
3355484 AAAAATAATTCAATTAAGTCCCTAGACTTAATGAAAATTTAAAATTGAGTTGCAAATTAAAACTT
1 AAAAATAATTCAATTAAGTCCCTAGACTTAATGAAAATTTAAAATTGAGTTGCAAATTAAAACTT
* *
3355549 GGATCAAAATTGGCCCTTTTATTTGAAATTAAAAATTTATTTTTCCATTTAGGGGATAATTTCTT
66 GGATCAAAATTGACCCTTTTATTTGAAACTAAAAATTTATTTTTCCATTTAGGGGATAATTTCTT
*
3355614 GGAAAATTATGTCAAAATAAATTCTCAAGAAAGATTGGAGGGGTCACAAACGGTCCCACTTAACT
131 GGAAAATTATGTCAAAATAAATTCCCAAGAAAGATTGGAGGGGTCACAAACGGTCCCACTTAACT
3355679 A
196 A
3355680 AAAAATAATTCAATTAAGTCCCTAGACTTAATGAAAATTTAAAATTGAGTTGCAAATTAAAACTT
1 AAAAATAATTCAATTAAGTCCCTAGACTTAATGAAAATTTAAAATTGAGTTGCAAATTAAAACTT
*
3355745 GGATCAAAATTGACCCTTTTATTTGAAACTAAAAATTTATTTTTCCCTTTAGGGGATAATTTCTT
66 GGATCAAAATTGACCCTTTTATTTGAAACTAAAAATTTATTTTTCCATTTAGGGGATAATTTCTT
* *
3355810 GGAAAATTATGTCAAAATAAATTCCCAGGAATGATTGGAGGGGTCACAAACGGTCCCACTTAA
131 GGAAAATTATGTCAAAATAAATTCCCAAGAAAGATTGGAGGGGTCACAAACGGTCCCACTTAA
3355873 GTTCCAATCT
Statistics
Matches: 187, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
196 187 1.00
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (196 bp):
AAAAATAATTCAATTAAGTCCCTAGACTTAATGAAAATTTAAAATTGAGTTGCAAATTAAAACTT
GGATCAAAATTGACCCTTTTATTTGAAACTAAAAATTTATTTTTCCATTTAGGGGATAATTTCTT
GGAAAATTATGTCAAAATAAATTCCCAAGAAAGATTGGAGGGGTCACAAACGGTCCCACTTAACT
A
Found at i:3363049 original size:11 final size:11
Alignment explanation
Indices: 3362999--3363051 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
3362989 ATAAAAGTTC
3362999 TAAAATA-AAT
1 TAAAATAGAAT
3363009 TAAATATATGAAT
1 TAAA-ATA-GAAT
*
3363022 TCAAAATAGACT
1 T-AAAATAGAAT
*
3363034 CAAAATAGAAT
1 TAAAATAGAAT
3363045 TAAAATA
1 TAAAATA
3363052 ACCATTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (11 bp):
TAAAATAGAAT
Found at i:3364878 original size:50 final size:50
Alignment explanation
Indices: 3364748--3365406 Score: 472
Period size: 50 Copynumber: 13.2 Consensus size: 50
3364738 TAACTCGTAA
* ** * * **
3364748 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGATTTGCTGTTGTAG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGTTGTAG
* * ** * ** * *
3364798 CTTCAATCTGTTCCACT-AAACCTCCTGGGAAGTAAGATTCGCTGTTGTAG
1 CTTTAATCTTTTTAACTGCAATGT-CGGGGAAGTAAGATTCACTGTTGTAG
* * * ** *
3364848 CATTAATCTTTTTAACTACAATGTCGGGGAAGCAAGATTCACCAATT-TGG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCA-CTGTTGTAG
* ** * * * *
3364898 CTTTAATCTGTTCCACTGC-ATCGCCAGGGAAATAAGATTCGCTGTTGTAG
1 CTTTAATCTTTTTAACTGCAAT-GTCGGGGAAGTAAGATTCACTGTTGTAG
* * * *
3364948 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGTTGTAG
* ** * * * *
3364998 CTTTAATCTGTTCCACTGC-ATCGCCAGGGAAATAAGATTCGCTGTTGTAG
1 CTTTAATCTTTTTAACTGCAAT-GTCGGGGAAGTAAGATTCACTGTTGTAG
* * * * *
3365048 CTTTAATCTTTTTAACTACAATGTCGGGGAAGAAAGATTCACCGATGTGG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGTTGTAG
* ** ** * * * *
3365098 CTTTAATCTGTTCCACTGCACCGCCAGGGAAATAAGATTCGCTGTTGTAG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGTTGTAG
* * *
3365148 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGATGTGG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGTTGTAG
** ** *
3365198 CTTTAAT-TTGTTCCACTGC-ATCACCTGGGG-AGTAAGATTCGCTGTTGTAG
1 CTTTAATCTT-TTTAACTGCAAT-GTC-GGGGAAGTAAGATTCACTGTTGTAG
* * * * *
3365248 CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTGG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGTTGTAG
* ** * * * *
3365298 CTTTAATCTGTTCCAGTGC-ATCGCTTGGGG-AGTAAGATTCACCGTTATAG
1 CTTTAATCTTTTTAACTGCAAT-G-TCGGGGAAGTAAGATTCACTGTTGTAG
* * * *
3365348 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACTGATGTGG
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGTTGTAG
3365398 CTTTAATCT
1 CTTTAATCT
3365407 GTTCCACTGG
Statistics
Matches: 454, Mismatches: 137, Indels: 36
0.72 0.22 0.06
Matches are distributed among these distances:
49 22 0.05
50 408 0.90
51 24 0.05
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (50 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGTAAGATTCACTGTTGTAG
Found at i:3364928 original size:100 final size:100
Alignment explanation
Indices: 3364748--3365432 Score: 1001
Period size: 100 Copynumber: 6.8 Consensus size: 100
3364738 TAACTCGTAA
* ** * ** * * * *
3364748 CTTTAATCTGTTTAACTGTGATGTCGAGGAAGCAAGATTTGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
** * *
3364813 CTAAACCTCCTGGGAAGTAAGATTCGCTGTTGTAG
66 CTGCATCGCCTGGGAAGTAAGATTCGCTGTTGTAG
* * * *
3364848 CATTAATCTTTTTAACTACAATGTCGGGGAAGCAAGATTCACCAATTTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* *
3364913 CTGCATCGCCAGGGAAATAAGATTCGCTGTTGTAG
66 CTGCATCGCCTGGGAAGTAAGATTCGCTGTTGTAG
3364948 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* *
3365013 CTGCATCGCCAGGGAAATAAGATTCGCTGTTGTAG
66 CTGCATCGCCTGGGAAGTAAGATTCGCTGTTGTAG
* *
3365048 CTTTAATCTTTTTAACTACAATGTCGGGGAAGAAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * *
3365113 CTGCACCGCCAGGGAAATAAGATTCGCTGTTGTAG
66 CTGCATCGCCTGGGAAGTAAGATTCGCTGTTGTAG
* *
3365148 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACTGATGTGGCTTTAATTTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* *
3365213 CTGCATCACCTGGGGAGTAAGATTCGCTGTTGTAG
66 CTGCATCGCCTGGGAAGTAAGATTCGCTGTTGTAG
*
3365248 CTTTAATCTTTTTAACTGCAATGTCGAGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
* * * * * *
3365313 GTGCATCGCTTGGGGAGTAAGATTCACCGTTATAG
66 CTGCATCGCCTGGGAAGTAAGATTCGCTGTTGTAG
* *
3365348 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACTGATGTGGCTTTAATCTGTTCCA
1 CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
*
3365413 CTGGATCGCCTGGGAAGTAA
66 CTGCATCGCCTGGGAAGTAA
3365433 AACTGGTATT
Statistics
Matches: 533, Mismatches: 52, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
100 533 1.00
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (100 bp):
CTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCA
CTGCATCGCCTGGGAAGTAAGATTCGCTGTTGTAG
Found at i:3366740 original size:8 final size:7
Alignment explanation
Indices: 3366720--3366783 Score: 71
Period size: 7 Copynumber: 9.0 Consensus size: 7
3366710 TTAACCTCTC
3366720 CATTTTT
1 CATTTTT
3366727 -ACTTTTT
1 CA-TTTTT
3366734 CATTTTTT
1 CA-TTTTT
3366742 CATTTTT
1 CATTTTT
3366749 CA-TTTT
1 CATTTTT
3366755 CA-TTTT
1 CATTTTT
3366761 CATTTTTT
1 CA-TTTTT
3366769 CATTTTT
1 CATTTTT
3366776 CATATTTT
1 CAT-TTTT
3366784 TTCTAACTCA
Statistics
Matches: 51, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
6 13 0.25
7 20 0.39
8 18 0.35
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (7 bp):
CATTTTT
Found at i:3367653 original size:21 final size:22
Alignment explanation
Indices: 3367627--3367671 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3367617 TGGCCTCTCC
* *
3367627 TTTTCTTTTCT-TTTTTTCCTT
1 TTTTCTTCTCTCTTTTTTCATT
3367648 TTTTCTTCTCTCTTTTTTCATT
1 TTTTCTTCTCTCTTTTTTCATT
3367670 TT
1 TT
3367672 CATTTTTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTTCTTCTCTCTTTTTTCATT
Found at i:3367699 original size:35 final size:33
Alignment explanation
Indices: 3367660--3367766 Score: 105
Period size: 35 Copynumber: 3.2 Consensus size: 33
3367650 TTCTTCTCTC
3367660 TTTTTTCATTTTCATTTTTTTGACTTTGATTTTGA
1 TTTTTTCATTTTC-TTTTTTTG-CTTTGATTTTGA
*
3367695 TTTTTTC-TCTTTCTTTTTTTTGTTTTTGATTTTGA
1 TTTTTTCAT-TTTC-TTTTTTTG-CTTTGATTTTGA
*
3367730 --TTTTGATTTT-TTCTTTTTGCTTTTGATTTTGA
1 TTTTTTCATTTTCTT-TTTTTGC-TTTGATTTTGA
3367762 TTTTT
1 TTTTT
3367767 ATTTTTATTC
Statistics
Matches: 61, Mismatches: 5, Indels: 13
0.77 0.06 0.16
Matches are distributed among these distances:
31 2 0.03
32 17 0.28
33 7 0.11
34 5 0.08
35 30 0.49
ACGTcount: A:0.09, C:0.07, G:0.09, T:0.74
Consensus pattern (33 bp):
TTTTTTCATTTTCTTTTTTTGCTTTGATTTTGA
Found at i:3367747 original size:20 final size:20
Alignment explanation
Indices: 3367684--3367759 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
3367674 TTTTTTTGAC
*
3367684 TTTGATTTTGATTTTTTCTC
1 TTTGATTTTGATTTTTTCTT
** ** **
3367704 TTTCTTTTTTTTGTTTTTGAT
1 TTTGATTTTGAT-TTTTTCTT
3367725 TTTGATTTTGATTTTTTCTT
1 TTTGATTTTGATTTTTTCTT
*
3367745 TTTGCTTTTGATTTT
1 TTTGATTTTGATTTT
3367760 GATTTTTATT
Statistics
Matches: 41, Mismatches: 14, Indels: 2
0.72 0.25 0.04
Matches are distributed among these distances:
20 28 0.68
21 13 0.32
ACGTcount: A:0.08, C:0.07, G:0.11, T:0.75
Consensus pattern (20 bp):
TTTGATTTTGATTTTTTCTT
Found at i:3367772 original size:26 final size:26
Alignment explanation
Indices: 3367710--3367766 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
3367700 TCTCTTTCTT
*
3367710 TTTTTTGTTTTTGATTTTGATTTTGA
1 TTTTTTCTTTTTGATTTTGATTTTGA
*
3367736 TTTTTTCTTTTTGCTTTTGATTTTGA
1 TTTTTTCTTTTTGATTTTGATTTTGA
3367762 TTTTT
1 TTTTT
3367767 ATTTTTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.09, C:0.04, G:0.12, T:0.75
Consensus pattern (26 bp):
TTTTTTCTTTTTGATTTTGATTTTGA
Found at i:3369810 original size:24 final size:21
Alignment explanation
Indices: 3369761--3369811 Score: 57
Period size: 24 Copynumber: 2.3 Consensus size: 21
3369751 CCATCATGTT
3369761 TTCTTGGATTTTATCTAACCG
1 TTCTTGGATTTTATCTAACCG
* *
3369782 CTCTTGGATTTGTACTTGTAACCG
1 TTCTTGGATTT-TA--TCTAACCG
3369806 TTCTTG
1 TTCTTG
3369812 CATATCCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.42
22 2 0.08
24 12 0.50
ACGTcount: A:0.16, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TTCTTGGATTTTATCTAACCG
Found at i:3372004 original size:11 final size:11
Alignment explanation
Indices: 3371954--3372006 Score: 54
Period size: 11 Copynumber: 4.6 Consensus size: 11
3371944 ATAAAAGTTA
3371954 TAAAATA-AAT
1 TAAAATAGAAT
3371964 TAAATATATGAAT
1 TAAA-ATA-GAAT
*
3371977 TCAAAATAGACT
1 T-AAAATAGAAT
*
3371989 CAAAATAGAAT
1 TAAAATAGAAT
3372000 TAAAATA
1 TAAAATA
3372007 ACCATTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
10 4 0.11
11 18 0.51
12 3 0.09
13 7 0.20
14 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.28
Consensus pattern (11 bp):
TAAAATAGAAT
Found at i:3374684 original size:18 final size:19
Alignment explanation
Indices: 3374651--3374691 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
3374641 ATGTTCATAT
*
3374651 TTTTAACATAATTTAATTA
1 TTTTAAAATAATTTAATTA
3374670 TTTTAAAAT-ATTTAATTA
1 TTTTAAAATAATTTAATTA
3374688 TTTT
1 TTTT
3374692 TTGACAAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTAAAATAATTTAATTA
Found at i:3386315 original size:46 final size:47
Alignment explanation
Indices: 3386265--3386385 Score: 128
Period size: 46 Copynumber: 2.6 Consensus size: 47
3386255 ATCATGTTTG
*
3386265 TTATTTCT-AATTTATCA-ATATTAT-TATTTTAAATTCATCATTAACT
1 TTATTT-TAAATTTATCATATA-TATCTATTTCAAATTCATCATTAACT
* *
3386311 TTATTTTAAATTTATCATGTATATCTATTTCAAATTTATCATTAA-T
1 TTATTTTAAATTTATCATATATATCTATTTCAAATTCATCATTAACT
* *
3386357 AT-TTTTAAATTTATTATATACTAT-TATTT
1 TTATTTTAAATTTATCATATA-TATCTATTT
3386386 TGGATTTATC
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
45 22 0.34
46 23 0.35
47 20 0.31
ACGTcount: A:0.35, C:0.08, G:0.01, T:0.56
Consensus pattern (47 bp):
TTATTTTAAATTTATCATATATATCTATTTCAAATTCATCATTAACT
Found at i:3386315 original size:69 final size:69
Alignment explanation
Indices: 3386235--3386396 Score: 186
Period size: 69 Copynumber: 2.3 Consensus size: 69
3386225 AAGTGTATTG
* * * * *
3386235 TATATTATTATTTTAGATTTATCATGTTTGT-TATTTCTAATTTATCAATATTATTATTTTAAAT
1 TATACTATTATTTTAGATTTATCATGTATATCTATTTCAAATTTATCAATAATA-T-TTTTAAAT
3386299 TCATCA
64 TCATCA
* *
3386305 T-TAACT-TTATTTTAAATTTATCATGTATATCTATTTCAAATTTATCATTAATATTTTTAAATT
1 TAT-ACTATTATTTTAGATTTATCATGTATATCTATTTCAAATTTATCAATAATATTTTTAAATT
* *
3386368 TATTA
65 CATCA
*
3386373 TATACTATTATTTTGGATTTATCA
1 TATACTATTATTTTAGATTTATCA
3386397 CGTAAGATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 9
0.79 0.11 0.09
Matches are distributed among these distances:
68 16 0.21
69 39 0.51
70 22 0.29
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (69 bp):
TATACTATTATTTTAGATTTATCATGTATATCTATTTCAAATTTATCAATAATATTTTTAAATTC
ATCA
Found at i:3386345 original size:24 final size:23
Alignment explanation
Indices: 3386240--3386385 Score: 97
Period size: 23 Copynumber: 6.3 Consensus size: 23
3386230 TATTGTATAT
* * *
3386240 TATTATTTTAGATTTATCATGTT
1 TATTATTTCAAATTTATCATGTA
* * *
3386263 TGTTATTTCTAATTTATCA-ATA
1 TATTATTTCAAATTTATCATGTA
* *
3386285 TTATTATTTTAAATTCATCAT-TA
1 -TATTATTTCAAATTTATCATGTA
*
3386308 -ACTTTATTTTAAATTTATCATGTA
1 TA--TTATTTCAAATTTATCATGTA
3386332 TATCTATTTCAAATTTATCAT-TAA
1 TAT-TATTTCAAATTTATCATGT-A
* *
3386356 TATT-TTT-AAATTTATTATATA
1 TATTATTTCAAATTTATCATGTA
3386377 CTATTATTT
1 -TATTATTT
3386386 TGGATTTATC
Statistics
Matches: 99, Mismatches: 13, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
21 12 0.12
22 9 0.09
23 55 0.56
24 22 0.22
25 1 0.01
ACGTcount: A:0.33, C:0.08, G:0.03, T:0.57
Consensus pattern (23 bp):
TATTATTTCAAATTTATCATGTA
Found at i:3392665 original size:39 final size:39
Alignment explanation
Indices: 3392622--3392699 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
3392612 AAGAATACCA
3392622 ACATTTCAGCAAATTTCTGGACAAATAAGAAACCTGAAG
1 ACATTTCAGCAAATTTCTGGACAAATAAGAAACCTGAAG
3392661 ACATTTCAGCAAATTTCTGGACAAATAAGAAACCTGAAG
1 ACATTTCAGCAAATTTCTGGACAAATAAGAAACCTGAAG
3392700 GTACATGGTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (39 bp):
ACATTTCAGCAAATTTCTGGACAAATAAGAAACCTGAAG
Found at i:3393574 original size:308 final size:309
Alignment explanation
Indices: 3393015--3393629 Score: 1214
Period size: 308 Copynumber: 2.0 Consensus size: 309
3393005 TCCAACACAT
3393015 ATGTCACTGTAATATGCTGAGTTAGAAAGCAAAAGAGTGACTGTTTAGACAAGACCGAACATTAC
1 ATGTCACTGTAATATGCTGAGTTAGAAAGCAAAAGAGTGACTGTTTAGACAAGACCGAACATTAC
3393080 TTAAGTATTAAATATAACGTATAATGTATATAATTATCATGACAGAAGGAAATGGTATGATAATT
66 TTAAGTATTAAATATAACGTATAATGTATATAATTATCATGACAGAAGGAAATGGTATGATAATT
3393145 TTTCTCCGAAAATTAACAGGTTTTGAAATGTCTACACTTTCAGTGAACAGATATAGACCATAAAC
131 TTTCTCCGAAAATTAACAGGTTTTGAAATGTCTACACTTTCAGTGAACAGATATAGACCATAAAC
3393210 CTCAATAAGCAAGTACCTGCTACATAGCATCTTAATTTTTGGAATCAGGAAATGTTAGCTTCGTA
196 CTCAATAAGCAAGTACCTGCTACATAGCATCTTAATTTTTGGAATCAGGAAATGTTAGCTTCGTA
3393275 TTTTATGACTTTCAGAAGTTTTCTAGAAAACTTTAATACAGCTACAAAC
261 TTTTATGACTTTCAGAAGTTTTCTAGAAAACTTTAATACAGCTACAAAC
3393324 ATGTCACTGTAATATGCTGAGTTAGAAAGCAAAAGAGTGACTG-TTAGACAAGACCGAACATTAC
1 ATGTCACTGTAATATGCTGAGTTAGAAAGCAAAAGAGTGACTGTTTAGACAAGACCGAACATTAC
3393388 TTAAGTATTAAATATAACGTATAATGTATATAATTATCATGACAGAAGGAAATGGTATGATAATT
66 TTAAGTATTAAATATAACGTATAATGTATATAATTATCATGACAGAAGGAAATGGTATGATAATT
3393453 TTTCTCCGAAAATTAACAGGTTTTGAAATGTCTACACTTTCAGTGAACAGATATAGACCATAAAC
131 TTTCTCCGAAAATTAACAGGTTTTGAAATGTCTACACTTTCAGTGAACAGATATAGACCATAAAC
3393518 CTCAATAAGCAAGTACCTGCTACATAGCATCTTAATTTTTGGAATCAGGAAATGTTAGCTTCGTA
196 CTCAATAAGCAAGTACCTGCTACATAGCATCTTAATTTTTGGAATCAGGAAATGTTAGCTTCGTA
*
3393583 TTTTATGACTTTCAGAAGTTTTCTAGAAAAGTTTAATACAGCTACAA
261 TTTTATGACTTTCAGAAGTTTTCTAGAAAACTTTAATACAGCTACAA
3393630 GCCAACGACC
Statistics
Matches: 305, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
308 262 0.86
309 43 0.14
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (309 bp):
ATGTCACTGTAATATGCTGAGTTAGAAAGCAAAAGAGTGACTGTTTAGACAAGACCGAACATTAC
TTAAGTATTAAATATAACGTATAATGTATATAATTATCATGACAGAAGGAAATGGTATGATAATT
TTTCTCCGAAAATTAACAGGTTTTGAAATGTCTACACTTTCAGTGAACAGATATAGACCATAAAC
CTCAATAAGCAAGTACCTGCTACATAGCATCTTAATTTTTGGAATCAGGAAATGTTAGCTTCGTA
TTTTATGACTTTCAGAAGTTTTCTAGAAAACTTTAATACAGCTACAAAC
Found at i:3393947 original size:2 final size:2
Alignment explanation
Indices: 3393940--3393966 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3393930 AGAACAAGCA
3393940 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 A
3393967 AGAAAAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3394903 original size:3 final size:3
Alignment explanation
Indices: 3394895--3394953 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
3394885 TTTTCATGGT
3394895 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3394943 TTA TTA TTA TT
1 TTA TTA TTA TT
3394954 TTTGCCTCTG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3395293 original size:29 final size:29
Alignment explanation
Indices: 3395261--3395317 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3395251 AAAAAGCTTT
*
3395261 TTTTTTCAA-AATTTATTGAAATGGACCAC
1 TTTTTT-AATAATTTATCGAAATGGACCAC
* *
3395290 TTTTTTAATTATTTATCGGAATGGACCA
1 TTTTTTAATAATTTATCGAAATGGACCA
3395318 TTTCCGCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (29 bp):
TTTTTTAATAATTTATCGAAATGGACCAC
Found at i:3402180 original size:29 final size:28
Alignment explanation
Indices: 3402122--3402182 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
3402112 GATTTCGCGG
3402122 AAAATGGCCAATTCCGGTAAATAATTAAA
1 AAAATGGCCAATTCCGGTAAATAA-TAAA
* * * **
3402151 AAAGTGGCCCATTTCGGTAAATTGTAAA
1 AAAATGGCCAATTCCGGTAAATAATAAA
3402179 AAAA
1 AAAA
3402183 AATGGCTTTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (28 bp):
AAAATGGCCAATTCCGGTAAATAATAAA
Found at i:3402304 original size:16 final size:16
Alignment explanation
Indices: 3402283--3402313 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3402273 TGCTGTATTA
3402283 GAATAGAGGCGTAATG
1 GAATAGAGGCGTAATG
3402299 GAATAGAGGCGTAAT
1 GAATAGAGGCGTAAT
3402314 AGCAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.06, G:0.35, T:0.19
Consensus pattern (16 bp):
GAATAGAGGCGTAATG
Found at i:3402562 original size:16 final size:16
Alignment explanation
Indices: 3402525--3402566 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
3402515 TTAATCATAT
*
3402525 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
3402541 TT-AAATATATTATAA
1 TTAAAATATATTATAA
3402556 TTAAAATATAT
1 TTAAAATATAT
3402567 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:3402573 original size:14 final size:15
Alignment explanation
Indices: 3402534--3402575 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
3402524 TTTAAACATA
*
3402534 ATTATTATTAAATAT
1 ATTATAATTAAATAT
3402549 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
3402563 A-TATAATTTAATA
1 ATTATAATTAAATA
3402576 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:3408583 original size:107 final size:107
Alignment explanation
Indices: 3408396--3408685 Score: 472
Period size: 107 Copynumber: 2.7 Consensus size: 107
3408386 ACAAATCAAG
* * *
3408396 TTCCAATTTCATATTCTATTGACTAACAAATCAAGAACAATTTCCAGCAGACAATCAAAACAATT
1 TTCCAATTTCATCTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATT
* *
3408461 TCCAGAACAAATCAAGAATAATATCAAAACAAATGCAACAAT
66 TCCAGAACAAATCAAGAACAAAATCAAAACAAATGCAACAAT
* *
3408503 TTCCAGTTTCATCTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAACT
1 TTCCAATTTCATCTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATT
* *
3408568 GCCAGAACAATTCAAGAACAAAATCAAAACAAATGCAACAAT
66 TCCAGAACAAATCAAGAACAAAATCAAAACAAATGCAACAAT
* * *
3408610 TTCCAATTTCATCTTCTACTCACTAACAAATCAATAACATTTTCCAGCAGACTATCAAAACAATT
1 TTCCAATTTCATCTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATT
3408675 TCCAGAACAAA
66 TCCAGAACAAA
3408686 CCAACAAAAT
Statistics
Matches: 167, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 167 1.00
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (107 bp):
TTCCAATTTCATCTTCTACTGACTAACAAATCAAGAACAATTTCCAGCAGACTATCAAAACAATT
TCCAGAACAAATCAAGAACAAAATCAAAACAAATGCAACAAT
Found at i:3420769 original size:11 final size:11
Alignment explanation
Indices: 3420753--3420777 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3420743 CTTACTTTAA
3420753 GGAAAGTGGGT
1 GGAAAGTGGGT
3420764 GGAAAGTGGGT
1 GGAAAGTGGGT
3420775 GGA
1 GGA
3420778 TGGCTTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.56, T:0.16
Consensus pattern (11 bp):
GGAAAGTGGGT
Found at i:3425455 original size:25 final size:25
Alignment explanation
Indices: 3425427--3425476 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3425417 CTTATGCAAT
* *
3425427 ATGCATATTTAACTATGATTTCATC
1 ATGCATATTCAACTATCATTTCATC
3425452 ATGCATATTCAACTATCATTTCATC
1 ATGCATATTCAACTATCATTTCATC
3425477 TTCCATCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.32, C:0.20, G:0.06, T:0.42
Consensus pattern (25 bp):
ATGCATATTCAACTATCATTTCATC
Found at i:3425493 original size:26 final size:25
Alignment explanation
Indices: 3425430--3425493 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
3425420 ATGCAATATG
* * *
3425430 CATATTTAACTATGATTTCATCATG
1 CATATTCAACTATCATTTCATCATC
*
3425455 CATATTCAACTATCATTTCATCTTC
1 CATATTCAACTATCATTTCATCATC
*
3425480 CATCATTCAGCTAT
1 CAT-ATTCAACTAT
3425494 ATTAAATCAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
25 24 0.73
26 9 0.27
ACGTcount: A:0.30, C:0.23, G:0.05, T:0.42
Consensus pattern (25 bp):
CATATTCAACTATCATTTCATCATC
Found at i:3426076 original size:30 final size:30
Alignment explanation
Indices: 3426043--3426239 Score: 143
Period size: 30 Copynumber: 6.6 Consensus size: 30
3426033 AATCAAAGTT
* *
3426043 ATCCCTTTTCATAGTTCGACAGCTGAAGCT
1 ATCCCTTTTCATAGTTCGATAGCTGAAGCC
* * * * *
3426073 ATCCCTTTTCATAATTTGATGGTTGTCA-CC
1 ATCCCTTTTCATAGTTCGATAGCTG-AAGCC
* * * *
3426103 ATCCCTTTTCATTGTTTGAT-GGTCGTTA-CC
1 ATCCCTTTTCATAGTTCGATAGCT-G-AAGCC
* * * * *
3426133 ATCCCTTTTCATAATTTGATAGCCGAAACT
1 ATCCCTTTTCATAGTTCGATAGCTGAAGCC
*
3426163 ATCCCTTTTCATAGATC-ACTAGCTGAAGCC
1 ATCCCTTTTCATAGTTCGA-TAGCTGAAGCC
* *
3426193 ATCTCTTTTCATAGTTCAATAG-TCGAAGCC
1 ATCCCTTTTCATAGTTCGATAGCT-GAAGCC
3426223 ATCCCTTTTCATAGTTC
1 ATCCCTTTTCATAGTTC
3426240 AATGGTTGTC
Statistics
Matches: 134, Mismatches: 26, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
29 5 0.04
30 126 0.94
31 3 0.02
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (30 bp):
ATCCCTTTTCATAGTTCGATAGCTGAAGCC
Found at i:3426109 original size:60 final size:60
Alignment explanation
Indices: 3426043--3426331 Score: 189
Period size: 60 Copynumber: 4.9 Consensus size: 60
3426033 AATCAAAGTT
* * * *
3426043 ATCCCTTTTCATAGTTCGACAGCTGAAGCTATCCCTTTTCATAATTTGATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGACAGCTGAAGCCATCCCTTTTCATAATTTGATAGTCGTAACC
* * * * * * * *
3426103 ATCCCTTTTCATTGTTTGA-TGGTCGTTA-CCATCCCTTTTCATAATTTGATAGCCGAAACT
1 ATCCCTTTTCATAGTTCGACAGCT-G-AAGCCATCCCTTTTCATAATTTGATAGTCGTAACC
* * * **
3426163 ATCCCTTTTCATAGATC-ACTAGCTGAAGCCATCTCTTTTCATAGTTCAATAGTCG-AAGCC
1 ATCCCTTTTCATAGTTCGAC-AGCTGAAGCCATCCCTTTTCATAATTTGATAGTCGTAA-CC
* ** * * * * * *
3426223 ATCCCTTTTCATAGTTCAATGGTTGTCA-CCATCCCTTTTCAT-TTTTGATGGTCGTCACA
1 ATCCCTTTTCATAGTTCGACAGCTG-AAGCCATCCCTTTTCATAATTTGATAGTCGTAACC
* * * * * *
3426282 ATCCCTTTTCATA-ATCGATAGCCGAAGCTATCCCTTTCCGT-ATTTGATAG
1 ATCCCTTTTCATAGTTCGACAGCTGAAGCCATCCCTTTTCATAATTTGATAG
3426332 CCAAAGCTAT
Statistics
Matches: 172, Mismatches: 47, Indels: 22
0.71 0.20 0.09
Matches are distributed among these distances:
57 1 0.01
58 24 0.14
59 28 0.16
60 114 0.66
61 5 0.03
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.38
Consensus pattern (60 bp):
ATCCCTTTTCATAGTTCGACAGCTGAAGCCATCCCTTTTCATAATTTGATAGTCGTAACC
Found at i:3426240 original size:30 final size:29
Alignment explanation
Indices: 3426043--3426318 Score: 139
Period size: 30 Copynumber: 9.3 Consensus size: 29
3426033 AATCAAAGTT
* *
3426043 ATCCCTTTTCATAGTTCGACAG-CTGAAGCT
1 ATCCCTTTTCATAGTTCGATAGTC-GAA-CC
* * * * *
3426073 ATCCCTTTTCATAATTTGATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGATAGTCG-AACC
* * * *
3426103 ATCCCTTTTCATTGTTTGATGGTCGTTACC
1 ATCCCTTTTCATAGTTCGATAGTCG-AACC
* * * *
3426133 ATCCCTTTTCATAATTTGATAGCCGAAACT
1 ATCCCTTTTCATAGTTCGATAGTCG-AACC
*
3426163 ATCCCTTTTCATAGATC-ACTAG-CTGAAGCC
1 ATCCCTTTTCATAGTTCGA-TAGTC-GAA-CC
* *
3426193 ATCTCTTTTCATAGTTCAATAGTCGAAGCC
1 ATCCCTTTTCATAGTTCGATAGTCGAA-CC
* * * *
3426223 ATCCCTTTTCATAGTTCAATGGTTGTCACC
1 ATCCCTTTTCATAGTTCGATAGTCG-AACC
* * * * *
3426253 ATCCCTTTTCAT-TTTTGATGGTCGTCACA
1 ATCCCTTTTCATAGTTCGATAGTCG-AACC
* * *
3426282 ATCCCTTTTCATA-ATCGATAGCCGAAGCT
1 ATCCCTTTTCATAGTTCGATAGTCGAA-CC
3426311 ATCCCTTT
1 ATCCCTTT
3426319 CCGTATTTGA
Statistics
Matches: 197, Mismatches: 39, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
28 1 0.01
29 44 0.22
30 148 0.75
31 4 0.02
ACGTcount: A:0.22, C:0.26, G:0.13, T:0.38
Consensus pattern (29 bp):
ATCCCTTTTCATAGTTCGATAGTCGAACC
Found at i:3426314 original size:29 final size:29
Alignment explanation
Indices: 3426282--3426351 Score: 95
Period size: 29 Copynumber: 2.4 Consensus size: 29
3426272 GGTCGTCACA
*
3426282 ATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATAATCGATAGCCAAAGCT
* * * *
3426311 ATCCCTTTCCGTATTTGATAGCCAAAGCT
1 ATCCCTTTTCATAATCGATAGCCAAAGCT
3426340 ATCCCTTTTCAT
1 ATCCCTTTTCAT
3426352 TCGTCGATGA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.36
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCAAAGCT
Found at i:3426634 original size:17 final size:17
Alignment explanation
Indices: 3426612--3426644 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
3426602 TAATTTAGCC
3426612 CAAAATTCAT-ATTTTGG
1 CAAAATT-ATCATTTTGG
3426629 CAAAATTATCATTTTG
1 CAAAATTATCATTTTG
3426645 CCCCTATACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (17 bp):
CAAAATTATCATTTTGG
Found at i:3429049 original size:13 final size:13
Alignment explanation
Indices: 3429033--3429063 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3429023 TCTAAATATT
3429033 ATTAATGATAGAA
1 ATTAATGATAGAA
3429046 ATTAATGATAGAA
1 ATTAATGATAGAA
3429059 ATTAA
1 ATTAA
3429064 ATAACTAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (13 bp):
ATTAATGATAGAA
Found at i:3436150 original size:6 final size:6
Alignment explanation
Indices: 3436136--3436168 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
3436126 TTAAATCGAT
3436136 AAAAT- AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
3436169 GAATTTTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:3454709 original size:29 final size:27
Alignment explanation
Indices: 3454672--3454728 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 27
3454662 TAAAGTTTGA
*
3454672 TTAATTATTGATAACTATATAAAATAAAAT
1 TTAATTATTGAT-A-TAGAT-AAATAAAAT
3454702 TTAA-TATTGATATAGATAAATAAAAT
1 TTAATTATTGATATAGATAAATAAAAT
3454728 T
1 T
3454729 AGAAATCCTG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 10 0.38
27 4 0.15
28 1 0.04
29 7 0.27
30 4 0.15
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (27 bp):
TTAATTATTGATATAGATAAATAAAAT
Found at i:3454913 original size:29 final size:30
Alignment explanation
Indices: 3454870--3454947 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
3454860 AAGTTATAGA
* * *
3454870 TTTAGTCTCTATACTTTT-ATTTGATCAAT
1 TTTAGTCCCTGTACTTTTAAATTGATCAAT
* *
3454899 TTTAGTCCCTGTACTTTTCAAATTGGTCACT
1 TTTAGTCCCTGTACTTTT-AAATTGATCAAT
*
3454930 TTTAGTCCCTGTATTTTT
1 TTTAGTCCCTGTACTTTT
3454948 CAAAATTTGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
29 16 0.39
31 25 0.61
ACGTcount: A:0.19, C:0.18, G:0.10, T:0.53
Consensus pattern (30 bp):
TTTAGTCCCTGTACTTTTAAATTGATCAAT
Found at i:3454964 original size:31 final size:31
Alignment explanation
Indices: 3454896--3454966 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
3454886 TTATTTGATC
*
3454896 AATTTTAGTCCCTGTACTTTTCAAATTGGTC
1 AATTTTAGTCCCTGTACTTTTCAAATTGGTA
* * *
3454927 ACTTTTAGTCCCTGTATTTTTCAAAATTTG-A
1 AATTTTAGTCCCTGTACTTTTC-AAATTGGTA
3454958 AATTTTAGT
1 AATTTTAGT
3454967 ACTAACCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 28 0.82
32 6 0.18
ACGTcount: A:0.25, C:0.15, G:0.11, T:0.48
Consensus pattern (31 bp):
AATTTTAGTCCCTGTACTTTTCAAATTGGTA
Found at i:3460055 original size:13 final size:13
Alignment explanation
Indices: 3460037--3460064 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3460027 CAGTCCCAGA
3460037 AAACTTGTATTAC
1 AAACTTGTATTAC
3460050 AAACTTGTATTAC
1 AAACTTGTATTAC
3460063 AA
1 AA
3460065 TCTTTGCGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (13 bp):
AAACTTGTATTAC
Found at i:3471749 original size:43 final size:43
Alignment explanation
Indices: 3471683--3471878 Score: 207
Period size: 43 Copynumber: 4.6 Consensus size: 43
3471673 ACAGGTTATA
* * * * *
3471683 CTTCAGTTTATTTGATGATGCACTATAGGTGCCAGTATAATTG
1 CTTCGGTTTATTCGATGATGCACTACAGGTGCCAGTATATTTC
* *
3471726 CTTCGGTTTATTCGATGATGCACTACATGTGCTAGTATATTTC
1 CTTCGGTTTATTCGATGATGCACTACAGGTGCCAGTATATTTC
* * * *
3471769 CTTTGATTTA-TCTGATGATGCACTA-TGTGTGCTAGTATATTTC
1 CTTCGGTTTATTC-GATGATGCACTACAG-GTGCCAGTATATTTC
* * * *
3471812 CTTTGATTTATTCGATGATGCACTACATGTTCCAGTATATTTC
1 CTTCGGTTTATTCGATGATGCACTACAGGTGCCAGTATATTTC
* *
3471855 CTTCGGTTTATCCAATGATGCACT
1 CTTCGGTTTATTCGATGATGCACT
3471879 GAGGTGATAG
Statistics
Matches: 130, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
42 2 0.02
43 126 0.97
44 2 0.02
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.42
Consensus pattern (43 bp):
CTTCGGTTTATTCGATGATGCACTACAGGTGCCAGTATATTTC
Found at i:3471834 original size:86 final size:86
Alignment explanation
Indices: 3471689--3471878 Score: 256
Period size: 86 Copynumber: 2.2 Consensus size: 86
3471679 TATACTTCAG
* * *
3471689 TTTATTTGATGATGCACTATAGGTGCCAGTATAATTGCTTCGGTTTATTCGATGATGCACTACAT
1 TTTATCTGATGATGCACTATAGGTGCCAGTATAATTCCTTCGATTTATTCGATGATGCACTACAT
* *
3471754 GTGCTAGTATATTTCCTTTGA
66 GTGCCAGTATATTTCCTTCGA
* * *
3471775 TTTATCTGATGATGCACTAT-GTGTGCTAGTATATTTCCTTTGATTTATTCGATGATGCACTACA
1 TTTATCTGATGATGCACTATAG-GTGCCAGTATAATTCCTTCGATTTATTCGATGATGCACTACA
* *
3471839 TGTTCCAGTATATTTCCTTCGG
65 TGTGCCAGTATATTTCCTTCGA
**
3471861 TTTATCCAATGATGCACT
1 TTTATCTGATGATGCACT
3471879 GAGGTGATAG
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
85 1 0.01
86 90 0.99
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.43
Consensus pattern (86 bp):
TTTATCTGATGATGCACTATAGGTGCCAGTATAATTCCTTCGATTTATTCGATGATGCACTACAT
GTGCCAGTATATTTCCTTCGA
Found at i:3477783 original size:18 final size:18
Alignment explanation
Indices: 3477760--3477916 Score: 314
Period size: 18 Copynumber: 8.7 Consensus size: 18
3477750 AAAATGTGAG
3477760 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
3477778 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
3477796 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
3477814 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
3477832 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
3477850 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
3477868 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
3477886 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTT
3477904 AAATGATGTTCAC
1 AAATGATGTTCAC
3477917 CTTGATGGAA
Statistics
Matches: 139, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 139 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
AAATGATGTTCACATTTT
Found at i:3478434 original size:72 final size:72
Alignment explanation
Indices: 3478343--3478648 Score: 445
Period size: 72 Copynumber: 4.2 Consensus size: 72
3478333 CAATGCTAAA
3478343 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
3478408 GTGTAAT
66 GTGTAAT
* * *
3478415 CTAGTTTTATCAATGGTTGTTTATATTTGGTTTTTGGATATTAAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
3478480 GTGTAAT
66 GTGTAAT
* * * *
3478487 CTAGTTTTATCAATGGTTGTCTATGTTTGGTTTTTGGATGTTGAATTTATGGTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
*
3478552 GCT-TAAGG
66 G-TGTAA-T
* * *
3478560 CTAGTTTTATCAATAATTGTTTATGTTTAGTTTTTGGATATTGAATTTATATTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
****
3478625 ACAAAAT
66 GTGTAAT
3478632 -TAGTTTTATCAATAGTT
1 CTAGTTTTATCAATAGTT
3478649 TTTTTTATAT
Statistics
Matches: 210, Mismatches: 21, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
71 16 0.08
72 133 0.63
73 61 0.29
ACGTcount: A:0.24, C:0.07, G:0.16, T:0.54
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:3480396 original size:21 final size:21
Alignment explanation
Indices: 3480372--3480422 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
3480362 TACAACTGTG
3480372 TTAATATATA-ATTACAAATAT
1 TTAATATATATATT-CAAATAT
*
3480393 TTAATGAT-TATATTTAAATAT
1 TTAAT-ATATATATTCAAATAT
3480414 TTAA-ATATA
1 TTAATATATA
3480423 GTTTATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
19 2 0.08
20 2 0.08
21 17 0.65
22 5 0.19
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAATATATATATTCAAATAT
Found at i:3480702 original size:27 final size:27
Alignment explanation
Indices: 3480672--3480728 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
3480662 AACACTTAAA
3480672 TTTTAAACAAAACTTCTCAAAAGCACT
1 TTTTAAACAAAACTTCTCAAAAGCACT
** ** *
3480699 TTTTCCACAGCATTTCTCAAAAGCACT
1 TTTTAAACAAAACTTCTCAAAAGCACT
3480726 TTT
1 TTT
3480729 CAAAAGCACT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (27 bp):
TTTTAAACAAAACTTCTCAAAAGCACT
Found at i:3480731 original size:13 final size:13
Alignment explanation
Indices: 3480683--3480749 Score: 82
Period size: 13 Copynumber: 5.1 Consensus size: 13
3480673 TTTAAACAAA
*
3480683 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
3480696 ACTTTTTCCACAGC
1 AC-TTTTCAAAAGC
3480710 A-TTTCTCAAAAGC
1 ACTTT-TCAAAAGC
3480723 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
3480736 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
3480749 A
1 A
3480750 ATACTAAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
12 3 0.07
13 31 0.67
14 12 0.26
ACGTcount: A:0.36, C:0.27, G:0.07, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:3480736 original size:26 final size:28
Alignment explanation
Indices: 3480685--3480749 Score: 91
Period size: 26 Copynumber: 2.4 Consensus size: 28
3480675 TAAACAAAAC
* *
3480685 TTCTCAAAAGCACTTTTTCCACAGCA-T
1 TTCTCAAAAGCACTTTTTCAAAAGCACT
3480712 TTCTCAAAAGCAC-TTTTCAAAAGCACT
1 TTCTCAAAAGCACTTTTTCAAAAGCACT
3480739 TT-TCAAAAGCA
1 TTCTCAAAAGCA
3480750 ATACTAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 19 0.54
27 16 0.46
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (28 bp):
TTCTCAAAAGCACTTTTTCAAAAGCACT
Found at i:3492060 original size:20 final size:22
Alignment explanation
Indices: 3492037--3492087 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
3492027 ATTTATACAC
3492037 GCATTTTTTATA-AT-ATATAT
1 GCATTTTTTATATATAATATAT
3492057 GCATTTTTT-TATATAATATAT
1 GCATTTTTTATATATAATATAT
**
3492078 TTATTTTTTA
1 GCATTTTTTA
3492088 ACTCTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 2 0.08
20 11 0.42
21 13 0.50
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (22 bp):
GCATTTTTTATATATAATATAT
Found at i:3493932 original size:31 final size:31
Alignment explanation
Indices: 3493839--3493934 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
3493829 GGCAAATTAC
*
3493839 AAGAGTAATTGAATCCTAATAAAACTCTTTC
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
3493870 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
3493902 AAGAGTAATTGAATCCTAATAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAACTCTTTA
3493933 AA
1 AA
3493935 ATTATCTAAG
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.46, C:0.14, G:0.09, T:0.31
Consensus pattern (31 bp):
AAGAGTAATTGAATCCTAATAAAACTCTTTA
Found at i:3504569 original size:13 final size:14
Alignment explanation
Indices: 3504543--3504575 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3504533 TTAATGTTTC
3504543 TTTTATCTTATTAT
1 TTTTATCTTATTAT
3504557 TTTTATCTT-TTAT
1 TTTTATCTTATTAT
*
3504570 ATTTAT
1 TTTTAT
3504576 TTTACGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATCTTATTAT
Found at i:3504626 original size:15 final size:15
Alignment explanation
Indices: 3504606--3504634 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3504596 TTGAATAAAA
3504606 AAAAGAAAAGGAAAG
1 AAAAGAAAAGGAAAG
3504621 AAAAGAAAAGGAAA
1 AAAAGAAAAGGAAA
3504635 TGGTACTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGGAAAG
Found at i:3505102 original size:13 final size:14
Alignment explanation
Indices: 3505076--3505108 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3505066 TTAATGTTTC
3505076 TTTTATCTTATTAT
1 TTTTATCTTATTAT
3505090 TTTTATCTT-TTAT
1 TTTTATCTTATTAT
*
3505103 ATTTAT
1 TTTTAT
3505109 TTTACGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTTATCTTATTAT
Found at i:3505159 original size:15 final size:15
Alignment explanation
Indices: 3505139--3505167 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3505129 TTGAATAAAA
3505139 AAAAGAAAAGGAAAG
1 AAAAGAAAAGGAAAG
3505154 AAAAGAAAAGGAAA
1 AAAAGAAAAGGAAA
3505168 TGGTACTGAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGGAAAG
Found at i:3505483 original size:533 final size:534
Alignment explanation
Indices: 3504465--3505534 Score: 2133
Period size: 533 Copynumber: 2.0 Consensus size: 534
3504455 TTAGTAATTT
3504465 AATTTTTATTTAAATAAAATATTTTTCTTATTTATCCGCTCTCTTATTTCTATTCCCTTTAAATT
1 AATTTTTATTTAAATAAAATATTTTTCTTATTTATCCGCTCTCTTATTTCTATTCCCTTTAAATT
3504530 CAATTAATGTTTCTTTTATCTTATTATTTTTATCTTTTATATTTATTTTACGAAACATAGAAGCC
66 CAATTAATGTTTCTTTTATCTTATTATTTTTATCTTTTATATTTATTTTACGAAACATAGAAGCC
3504595 TTTGAATAAAAAAAAGAAAAGGAAAGAAAAGAAAAGGAAATGGTACTGACTGAATTTGTGACGGT
131 TTTGAATAAAAAAAAGAAAAGGAAAGAAAAGAAAAGGAAATGGTACTGACTGAATTTGTGACGGT
3504660 TTCGTTTTAATCAATTGTTTAAGAGCAGTTAAACCACATTCCATCTGCGAGCTCTGCACAATAAA
196 TTCGTTTTAATCAATTGTTTAAGAGCAGTTAAACCACATTCCATCTGCGAGCTCTGCACAATAAA
3504725 CAACGTGCTCGTTTAATTTTTTAATATATACTTTTTACCATAAGACATACACTTAATTTCAAATT
261 CAACGTGCTCGTTTAATTTTTTAATATATACTTTTTACCATAAGACATACACTTAATTTCAAATT
3504790 TAAAGCAAACTTTTATTTTAATATTCAACATTTTAAGAAGGAATGAAGTACGGAGTTTTGGTCCA
326 TAAAGCAAACTTTTATTTTAATATTCAACATTTTAAGAAGGAATGAAGTACGGAGTTTTGGTCCA
3504855 TTATATAGGCCACTACCACGCACGAATATAGTAATTTAATCTTATAAAATGCATAATATTTAGAC
391 TTATATAGGCCACTACCACGCACGAATATAGTAATTTAATCTTATAAAATGCATAATATTTAGAC
3504920 AAAGCAATCTTAGCCCCAATTTTCAAACCTCCAAGAAACAGAGAAACGAGACACATTCTTCTTTT
456 AAAGCAATCTTAGCCCCAATTTTCAAACCTCCAAGAAACAGAGAAACGAGACACATTCTTCTTTT
3504985 GACATAAATTTTTA
521 GACATAAATTTTTA
3504999 AATTTTTATTT-AATAAAATATTTTTCTTATTTATCCGCTCTCTTATTTCTATTCCCTTTAAATT
1 AATTTTTATTTAAATAAAATATTTTTCTTATTTATCCGCTCTCTTATTTCTATTCCCTTTAAATT
3505063 CAATTAATGTTTCTTTTATCTTATTATTTTTATCTTTTATATTTATTTTACGAAACATAGAAGCC
66 CAATTAATGTTTCTTTTATCTTATTATTTTTATCTTTTATATTTATTTTACGAAACATAGAAGCC
3505128 TTTGAATAAAAAAAAGAAAAGGAAAGAAAAGAAAAGGAAATGGTACTGACTGAATTTGTGACGGT
131 TTTGAATAAAAAAAAGAAAAGGAAAGAAAAGAAAAGGAAATGGTACTGACTGAATTTGTGACGGT
3505193 TTCGTTTTAATCAATTGTTTAAGAGCAGTTAAACCACATTCCATCTGCGAGCTCTGCACAATAAA
196 TTCGTTTTAATCAATTGTTTAAGAGCAGTTAAACCACATTCCATCTGCGAGCTCTGCACAATAAA
3505258 CAACGTGCTCGTTTAATTTTTTAATATATACTTTTTACCATAAGACATACACTTAATTTCAAATT
261 CAACGTGCTCGTTTAATTTTTTAATATATACTTTTTACCATAAGACATACACTTAATTTCAAATT
3505323 TAAAGCAAACTTTTATTTTAATATTCAACATTTTAAGAAGGAATGAAGTACGGAGTTTTGGTCCA
326 TAAAGCAAACTTTTATTTTAATATTCAACATTTTAAGAAGGAATGAAGTACGGAGTTTTGGTCCA
3505388 TTATATAGGCCACTACCACGCACGAATATAGTAATTTAATCTTATAAAATGCATAATATTTAGAC
391 TTATATAGGCCACTACCACGCACGAATATAGTAATTTAATCTTATAAAATGCATAATATTTAGAC
3505453 AAAGCAATCTTAGCCCCAATTTTCAAACCTCCAAGAAACAGAGAAACGAGACACATTCTTCTTTT
456 AAAGCAATCTTAGCCCCAATTTTCAAACCTCCAAGAAACAGAGAAACGAGACACATTCTTCTTTT
3505518 GACATAAATTTTTA
521 GACATAAATTTTTA
3505532 AAT
1 AAT
3505535 ATATTCCTGC
Statistics
Matches: 536, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
533 525 0.98
534 11 0.02
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (534 bp):
AATTTTTATTTAAATAAAATATTTTTCTTATTTATCCGCTCTCTTATTTCTATTCCCTTTAAATT
CAATTAATGTTTCTTTTATCTTATTATTTTTATCTTTTATATTTATTTTACGAAACATAGAAGCC
TTTGAATAAAAAAAAGAAAAGGAAAGAAAAGAAAAGGAAATGGTACTGACTGAATTTGTGACGGT
TTCGTTTTAATCAATTGTTTAAGAGCAGTTAAACCACATTCCATCTGCGAGCTCTGCACAATAAA
CAACGTGCTCGTTTAATTTTTTAATATATACTTTTTACCATAAGACATACACTTAATTTCAAATT
TAAAGCAAACTTTTATTTTAATATTCAACATTTTAAGAAGGAATGAAGTACGGAGTTTTGGTCCA
TTATATAGGCCACTACCACGCACGAATATAGTAATTTAATCTTATAAAATGCATAATATTTAGAC
AAAGCAATCTTAGCCCCAATTTTCAAACCTCCAAGAAACAGAGAAACGAGACACATTCTTCTTTT
GACATAAATTTTTA
Found at i:3505983 original size:9 final size:9
Alignment explanation
Indices: 3505962--3505998 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
3505952 GATTTTAAGG
3505962 TTTAGGG-T
1 TTTAGGGTT
3505970 TTTAGGGTT
1 TTTAGGGTT
*
3505979 TTTAGGATT
1 TTTAGGGTT
3505988 TTTAGGGTT
1 TTTAGGGTT
3505997 TT
1 TT
3505999 GAAGGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
8 7 0.27
9 19 0.73
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (9 bp):
TTTAGGGTT
Found at i:3510956 original size:18 final size:18
Alignment explanation
Indices: 3510918--3510953 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3510908 TTATTATTTT
*
3510918 TAAAATTTACTATTAAAA
1 TAAAATTTAATATTAAAA
3510936 TAAAATTTAAATATTAAA
1 TAAAATTT-AATATTAAA
3510954 TAATTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:3511159 original size:19 final size:19
Alignment explanation
Indices: 3511112--3511159 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 19
3511102 GAAAAAGACT
3511112 TATTTTCCGTTGACCTGTAAG
1 TATTTTCCGTTGACC--TAAG
3511133 TCATTTTCCGTTGACC-AAG
1 T-ATTTTCCGTTGACCTAAG
3511152 CTATTTTC
1 -TATTTTC
3511160 TATGAAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 9 0.36
20 1 0.04
21 1 0.04
22 14 0.56
ACGTcount: A:0.19, C:0.23, G:0.15, T:0.44
Consensus pattern (19 bp):
TATTTTCCGTTGACCTAAG
Found at i:3512376 original size:2 final size:2
Alignment explanation
Indices: 3512369--3512401 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3512359 AAAGAGTTTC
3512369 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
3512402 AGTATNNNNN
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:3512521 original size:16 final size:16
Alignment explanation
Indices: 3512500--3512540 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
3512490 NNNNNNNNNN
3512500 TATATATATATA-TATG
1 TATATATATA-AGTATG
3512516 TATATATATAAGTATG
1 TATATATATAAGTATG
*
3512532 TATGTATAT
1 TATATATAT
3512541 GGTATCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.04
16 22 0.96
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (16 bp):
TATATATATAAGTATG
Found at i:3515214 original size:51 final size:51
Alignment explanation
Indices: 3515091--3515278 Score: 209
Period size: 51 Copynumber: 3.7 Consensus size: 51
3515081 TATCATTCGA
* * * * * *
3515091 TACACGTAGTAACCTTCACATAGTACTACACACGTGATC-AAACTTTCCAG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCGG
* *
3515141 TTCACATAGTAGCCTGCACATAGTACTATACACGTGACCAAAACCTTCCGG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCGG
* * ** * *
3515192 TACACATAGTAGCCTACACATAGTACTACACATGTGACCATTATCTAT-CGA
1 TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCT-TCCGG
**
3515243 TACACATAGTAGCCTGCAGTTAGTACTACACACGTG
1 TACACATAGTAGCCTGCACATAGTACTACACACGTG
3515279 TTTATAGGCA
Statistics
Matches: 116, Mismatches: 20, Indels: 3
0.83 0.14 0.02
Matches are distributed among these distances:
50 33 0.28
51 82 0.71
52 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.14, T:0.26
Consensus pattern (51 bp):
TACACATAGTAGCCTGCACATAGTACTACACACGTGACCAAAACCTTCCGG
Found at i:3515222 original size:12 final size:13
Alignment explanation
Indices: 3515192--3515224 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
3515182 AACCTTCCGG
3515192 TACACATAGTAGCC
1 TACACATAGTA-CC
3515206 TACACATAGTA-C
1 TACACATAGTACC
3515218 TACACAT
1 TACACAT
3515225 GTGACCATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.42
14 11 0.58
ACGTcount: A:0.39, C:0.27, G:0.09, T:0.24
Consensus pattern (13 bp):
TACACATAGTACC
Found at i:3520325 original size:18 final size:18
Alignment explanation
Indices: 3520289--3520326 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3520279 AATTGTGTAA
* *
3520289 ATGGGGTAAATTTGTGAT
1 ATGGGGTAAATGTGAGAT
3520307 ATGGGGTAAATGTGAGAT
1 ATGGGGTAAATGTGAGAT
3520325 AT
1 AT
3520327 ATATGTTATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (18 bp):
ATGGGGTAAATGTGAGAT
Found at i:3520733 original size:10 final size:10
Alignment explanation
Indices: 3520718--3520774 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
3520708 TCCAAGTTCC
3520718 ATTTTATCTT
1 ATTTTATCTT
3520728 ATTTTAT-TT
1 ATTTTATCTT
3520737 CATTTTATCTT
1 -ATTTTATCTT
*
3520748 GTTTTATCTT
1 ATTTTATCTT
3520758 -TTCTTATCTT
1 ATT-TTATCTT
*
3520768 ATATTAT
1 ATTTTAT
3520775 ATGACTATGT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 4 0.10
10 34 0.83
11 3 0.07
ACGTcount: A:0.19, C:0.11, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTTATCTT
Found at i:3526969 original size:63 final size:63
Alignment explanation
Indices: 3526875--3527001 Score: 193
Period size: 62 Copynumber: 2.0 Consensus size: 63
3526865 AGAAATTATA
* *
3526875 AAAATGGAGAAATAGGAAACATTTGGAAATGATTATGGTTTTCTCCAACATTAAAATGAAAATG
1 AAAATGGAGAAATAGGAAACATTTGGAAATGAATATGG-TTTCTCCAAAATTAAAATGAAAATG
* * *
3526939 AAAATGGAGAAAT-GGAATCATTTGGAAATGAATGTGGTTTCTCCAAAATTTAAATGAAAATG
1 AAAATGGAGAAATAGGAAACATTTGGAAATGAATATGGTTTCTCCAAAATTAAAATGAAAATG
3527001 A
1 A
3527002 CCTGGAAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
62 24 0.41
63 21 0.36
64 13 0.22
ACGTcount: A:0.45, C:0.07, G:0.20, T:0.28
Consensus pattern (63 bp):
AAAATGGAGAAATAGGAAACATTTGGAAATGAATATGGTTTCTCCAAAATTAAAATGAAAATG
Found at i:3527521 original size:110 final size:110
Alignment explanation
Indices: 3527336--3527547 Score: 311
Period size: 110 Copynumber: 1.9 Consensus size: 110
3527326 GAGGGACGGA
* * *
3527336 AAACCCTAGTATTACTAACTAGGGTTGTGGGCCCCTATACTTCTAGTTAGACTAGGAGTTCATTT
1 AAACCCTAATATTACTAACTAGGGTTGTGGCCCCCTATACTACTAGTTAGACTAGGAGTTCATTT
*
3527401 TCTTAGTTGAAATAAAATTCTACAATTCAATAAGGGTGGGACAAC
66 TCTTAGTTGAAATAAAATTCTACAATTCAACAAGGGTGGGACAAC
* **
3527446 AAACCCTAATATTATTAACTAGGGTTGCT-GCCCCCTATACTACTAGTTAGACTAGGAGTTTGTT
1 AAACCCTAATATTACTAACTAGGGTTG-TGGCCCCCTATACTACTAGTTAGACTAGGAGTTCATT
* *
3527510 TT-TCTAGTTGAAATAAATTTCTATAATTCAACAAGGGT
65 TTCT-TAGTTGAAATAAAATTCTACAATTCAACAAGGGT
3527548 TCTACTTCTT
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
109 1 0.01
110 89 0.98
111 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (110 bp):
AAACCCTAATATTACTAACTAGGGTTGTGGCCCCCTATACTACTAGTTAGACTAGGAGTTCATTT
TCTTAGTTGAAATAAAATTCTACAATTCAACAAGGGTGGGACAAC
Found at i:3531281 original size:16 final size:16
Alignment explanation
Indices: 3531260--3531303 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
3531250 ATTCCACTAG
3531260 TATCCTTTTCAATTGA
1 TATCCTTTTCAATTGA
*
3531276 TATCCTTTTCATTTGA
1 TATCCTTTTCAATTGA
3531292 TATCCTTTTCAA
1 TATCCTTTTCAA
3531304 CCTTTTCATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.23, C:0.20, G:0.05, T:0.52
Consensus pattern (16 bp):
TATCCTTTTCAATTGA
Done.