Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008027.1 Hibiscus syriacus cultivar Beakdansim tig00110503_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 7662336
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 28 of 38
Found at i:5739295 original size:41 final size:41
Alignment explanation
Indices: 5739250--5739362 Score: 149
Period size: 41 Copynumber: 2.8 Consensus size: 41
5739240 TTTTTTATTA
5739250 TCGCATTGCGATAGTCA-GTA-TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGAT--TCACGTATTCGCATTGCGATTTTCCCAAT
* *
5739291 TCGCATTGCGATTTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTCACGTATTCGCATTGCGATTTTCCCAAT
* * *
5739332 TCGCGTTGCGATTTACTTATTCGCATTGCGA
1 TCGCATTGCGATTCACGTATTCGCATTGCGA
5739363 ATTGGGAAAA
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
39 2 0.03
40 2 0.03
41 63 0.94
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (41 bp):
TCGCATTGCGATTCACGTATTCGCATTGCGATTTTCCCAAT
Found at i:5739314 original size:20 final size:21
Alignment explanation
Indices: 5739270--5739362 Score: 109
Period size: 20 Copynumber: 4.5 Consensus size: 21
5739260 ATAGTCAGTA
*
5739270 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
**
5739291 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
*
5739311 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
* **
5739332 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
5739352 TCGCATTGCGA
1 TCGCATTGCGA
5739363 ATTGGGAAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 33 0.55
21 27 0.45
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:5753160 original size:96 final size:96
Alignment explanation
Indices: 5753042--5753239 Score: 387
Period size: 96 Copynumber: 2.1 Consensus size: 96
5753032 TAAACTTGAC
5753042 TCCCATTCGACCCGACACCGATCTGAACTCAATTTTTTTTTATTTTATAAAATCCGTCTCGTTTA
1 TCCC-TTCGACCCGACACCGATCTGAACTCAATTTTTTTTTATTTTATAAAATCCGTCTCGTTTA
5753107 TGACGAATTGGTCTGAACCGGTCGGATTCGAG
65 TGACGAATTGGTCTGAACCGGTCGGATTCGAG
5753139 TCCCTTCGACCCGACACCGATCTGAACTCAATTTTTTTTTATTTTATAAAATCCGTCTCGTTTAT
1 TCCCTTCGACCCGACACCGATCTGAACTCAATTTTTTTTTATTTTATAAAATCCGTCTCGTTTAT
5753204 GACGAATTGGTCTGAACCGGTCGGATTCGAG
66 GACGAATTGGTCTGAACCGGTCGGATTCGAG
5753235 TCCCT
1 TCCCT
5753240 GTCTCCAAGT
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 97 0.96
97 4 0.04
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (96 bp):
TCCCTTCGACCCGACACCGATCTGAACTCAATTTTTTTTTATTTTATAAAATCCGTCTCGTTTAT
GACGAATTGGTCTGAACCGGTCGGATTCGAG
Found at i:5754967 original size:33 final size:33
Alignment explanation
Indices: 5754930--5754998 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
5754920 TGGAGAATTC
5754930 GAGTTATTTATTGGAAGAATGCTAGTCAAAATG
1 GAGTTATTTATTGGAAGAATGCTAGTCAAAATG
*
5754963 GAGTTATTTATTGGAAGAGTGCTAGTCAAAATG
1 GAGTTATTTATTGGAAGAATGCTAGTCAAAATG
5754996 GAG
1 GAG
5754999 AATTTTCGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.35, C:0.06, G:0.28, T:0.32
Consensus pattern (33 bp):
GAGTTATTTATTGGAAGAATGCTAGTCAAAATG
Found at i:5755233 original size:39 final size:38
Alignment explanation
Indices: 5755159--5755234 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 38
5755149 ATACCTGAAG
*
5755159 TTTAGTTTTTGTTTCATTTTAGTATCGGTCGTTAAAAAT
1 TTTAGTTTTTGTTTCATTTTAGTATCCGTC-TTAAAAAT
5755198 TTTAGTTTTTGTTTCATTTTAGTACTCCCGT-TTAAAA
1 TTTAGTTTTTGTTTCATTTTAGTA-T-CCGTCTTAAAA
5755235 TTTAACGTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
39 30 0.88
40 1 0.03
41 3 0.09
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.54
Consensus pattern (38 bp):
TTTAGTTTTTGTTTCATTTTAGTATCCGTCTTAAAAAT
Found at i:5755442 original size:18 final size:19
Alignment explanation
Indices: 5755416--5755459 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
5755406 AGTTTATCGT
*
5755416 AAATAATTTT-AAAATAAA
1 AAATTATTTTAAAAATAAA
5755434 AAATTATTTTAAAAATAAA
1 AAATTATTTTAAAAATAAA
5755453 AATATTA
1 AA-ATTA
5755460 ATGTGAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 10 0.43
20 4 0.17
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTATTTTAAAAATAAA
Found at i:5766590 original size:67 final size:67
Alignment explanation
Indices: 5766519--5766652 Score: 162
Period size: 67 Copynumber: 2.0 Consensus size: 67
5766509 CACTTGACCC
* * *
5766519 GACCCGACCTGAAAAATATATATCCTAC-ACAGACTCCAACCGACCCAAATTTTTAGAATATAAA
1 GACCCAACCTGAAAAATATACATCCT-CTACAGACTCCAACCGACCCAAATTTTTAGAATAAAAA
5766583 TCT
65 TCT
* * * ** * *
5766586 GACCCAACTTGAAAAATATACATCCTCTCCCGACTCTGATCGACCCAAGTTTTTAGAATAAAAAT
1 GACCCAACCTGAAAAATATACATCCTCTACAGACTCCAACCGACCCAAATTTTTAGAATAAAAAT
5766651 CT
66 CT
5766653 AATCTGATAT
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
66 1 0.02
67 55 0.98
ACGTcount: A:0.38, C:0.27, G:0.10, T:0.25
Consensus pattern (67 bp):
GACCCAACCTGAAAAATATACATCCTCTACAGACTCCAACCGACCCAAATTTTTAGAATAAAAAT
CT
Found at i:5768306 original size:31 final size:32
Alignment explanation
Indices: 5768227--5768318 Score: 141
Period size: 32 Copynumber: 2.9 Consensus size: 32
5768217 ATTCTGTCCC
5768227 CTCATTTTCTATGATTAATTATACTTTGCCCT
1 CTCATTTTCTATGATTAATTATACTTTGCCCT
* *
5768259 CTCATTTTTTATGATTAATTGTACTTTGCCCT
1 CTCATTTTCTATGATTAATTATACTTTGCCCT
* *
5768291 CTCA-TTTGTATGATTAACTATACTTTGC
1 CTCATTTTCTATGATTAATTATACTTTGC
5768319 GCCCTTAAGT
Statistics
Matches: 55, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 21 0.38
32 34 0.62
ACGTcount: A:0.22, C:0.20, G:0.09, T:0.50
Consensus pattern (32 bp):
CTCATTTTCTATGATTAATTATACTTTGCCCT
Found at i:5769491 original size:76 final size:77
Alignment explanation
Indices: 5769386--5769548 Score: 222
Period size: 76 Copynumber: 2.1 Consensus size: 77
5769376 TGTGTCTTCA
* * * *
5769386 ACGTGGGGACTAGCTTTTTTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAA-GAAATTCATG
1 ACGTAGGGACCAGCTTTTGTTATGTTTGGTAGCAGGAAGTTTACAGCAAAATAAGGAAATT-ATG
5769450 GGAAGAATAATGC
65 GGAAGAATAATGC
* * * *
5769463 ATGTAGGGACCAGC-TTTGTTATGTTTGGTAGCATGATGTTTACAGGAAAATAAGGAAATTATGG
1 ACGTAGGGACCAGCTTTTGTTATGTTTGGTAGCAGGAAGTTTACAGCAAAATAAGGAAATTATGG
5769527 GAAGAATAATGC
66 GAAGAATAATGC
*
5769539 ACGTGGGGAC
1 ACGTAGGGAC
5769549 GGGAATGAGA
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
76 58 0.77
77 17 0.23
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (77 bp):
ACGTAGGGACCAGCTTTTGTTATGTTTGGTAGCAGGAAGTTTACAGCAAAATAAGGAAATTATGG
GAAGAATAATGC
Found at i:5770952 original size:16 final size:16
Alignment explanation
Indices: 5770896--5770953 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
5770886 AAATAATTAT
* *
5770896 AAAAATCAACAAAATA
1 AAAAATAAACATAATA
* *
5770912 AATAAATAAAAATATTA
1 AA-AAATAAACATAATA
* *
5770929 TAATATAAACATAATA
1 AAAAATAAACATAATA
5770945 AAAAATAAA
1 AAAAATAAA
5770954 TTTGCTTATT
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
16 20 0.65
17 11 0.35
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATAAACATAATA
Found at i:5772932 original size:76 final size:76
Alignment explanation
Indices: 5772806--5772967 Score: 270
Period size: 76 Copynumber: 2.1 Consensus size: 76
5772796 TCTCATTCTC
* * *
5772806 GTCCCCACGTGTATTATTCTTCCCATGATTTCCTTATTTTCCTGCAAACTTCATGCTACCAAACA
1 GTCCCCACGTGCATTATTCTTCCAATGAATTCCTTATTTTCCTGCAAACTTCATGCTACCAAACA
5772871 TAACAAAGCTG
66 TAACAAAGCTG
* *
5772882 GTCCCCACGTGCATTATTCTTCCAATGAATTCCTTATTTTCCTGCAAACTTCCTGCTACTAAACA
1 GTCCCCACGTGCATTATTCTTCCAATGAATTCCTTATTTTCCTGCAAACTTCATGCTACCAAACA
5772947 TAACAAAGCTG
66 TAACAAAGCTG
*
5772958 GTCTCCACGT
1 GTCCCCACGT
5772968 TGAAGACACA
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 80 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.33
Consensus pattern (76 bp):
GTCCCCACGTGCATTATTCTTCCAATGAATTCCTTATTTTCCTGCAAACTTCATGCTACCAAACA
TAACAAAGCTG
Found at i:5773070 original size:27 final size:23
Alignment explanation
Indices: 5773007--5773071 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 23
5772997 ATGCACATCT
*
5773007 GCTGAAGACGCCGAGATATCCAA
1 GCTGAAGACGCCGAGATATCAAA
*
5773030 GTTGAAGACGCCGAGAGCTCCATCAAA
1 GCTGAAGACGCCGAGA--T--ATCAAA
5773057 GCTGAAGACGCCGAG
1 GCTGAAGACGCCGAG
5773072 CTTTGCATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.43
25 1 0.03
27 19 0.54
ACGTcount: A:0.32, C:0.26, G:0.29, T:0.12
Consensus pattern (23 bp):
GCTGAAGACGCCGAGATATCAAA
Found at i:5774384 original size:11 final size:13
Alignment explanation
Indices: 5774347--5774385 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
5774337 TTTTCTTTTT
5774347 TAATATCATATTATA
1 TAATAT-ATA-TATA
5774362 TAATATATATATA
1 TAATATATATATA
*
5774375 TAATAAATATA
1 TAATATATATA
5774386 AAGTCGGAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 14 0.61
14 3 0.13
15 6 0.26
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (13 bp):
TAATATATATATA
Found at i:5774628 original size:3 final size:3
Alignment explanation
Indices: 5774620--5774734 Score: 230
Period size: 3 Copynumber: 38.3 Consensus size: 3
5774610 AACAAGTTAT
5774620 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
5774668 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
5774716 AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA A
5774735 AGAAAGAACA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 112 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:5776341 original size:29 final size:29
Alignment explanation
Indices: 5776286--5776341 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
5776276 TCAAAACCAT
* *
5776286 TCAAAAGTTATGGGATGAAACTGGAATAC
1 TCAAAAGTTATGGGAAGAAACTAGAATAC
*
5776315 TCAAAAGTTTTGGGAAGAATA-TAGAAT
1 TCAAAAGTTATGGGAAGAA-ACTAGAAT
5776342 GAGAGTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 22 0.96
30 1 0.04
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (29 bp):
TCAAAAGTTATGGGAAGAAACTAGAATAC
Found at i:5777489 original size:19 final size:19
Alignment explanation
Indices: 5777465--5777503 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5777455 CAGTTCGTAT
5777465 ATAACAAGAAACATATTTG
1 ATAACAAGAAACATATTTG
5777484 ATAACAAGAAACATATTTG
1 ATAACAAGAAACATATTTG
5777503 A
1 A
5777504 AGCACATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (19 bp):
ATAACAAGAAACATATTTG
Found at i:5783979 original size:2 final size:2
Alignment explanation
Indices: 5783972--5784035 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
5783962 TGTACACTAG
5783972 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5784014 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
5784036 GTCTGATCTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5792402 original size:18 final size:17
Alignment explanation
Indices: 5792379--5792412 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
5792369 CAGTCTGTTT
5792379 TATTTTAATGATTTTATA
1 TATTTTAAT-ATTTTATA
*
5792397 TATTTTGATATTTTAT
1 TATTTTAATATTTTAT
5792413 TTAATTATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTTTAATATTTTATA
Found at i:5799742 original size:2 final size:2
Alignment explanation
Indices: 5799735--5799761 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5799725 TTAAGATAAT
5799735 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5799762 TAAAACTACT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5812770 original size:23 final size:24
Alignment explanation
Indices: 5812725--5812771 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
5812715 TTATCTGCAA
* * *
5812725 TTAATCTTTTATAAAAGTTTAATT
1 TTAATCTTTAATAAAAATATAATT
5812749 TTAA-CTTTAATAAAAATATAATT
1 TTAATCTTTAATAAAAATATAATT
5812772 AAATTTATCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
TTAATCTTTAATAAAAATATAATT
Found at i:5814138 original size:29 final size:29
Alignment explanation
Indices: 5814097--5814172 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
5814087 AATGTTACAT
**
5814097 TTTTTTGGCCCAATAGGGCACCACTGTAA
1 TTTTTTGGCCCAATAGGGCACCACCATAA
*
5814126 TTTTTTGGCCCAATAGGGCACTACCATAA
1 TTTTTTGGCCCAATAGGGCACCACCATAA
*
5814155 TTATTTGGCCCAATAGGG
1 TTTTTTGGCCCAATAGGG
5814173 TACCTCAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (29 bp):
TTTTTTGGCCCAATAGGGCACCACCATAA
Found at i:5814185 original size:29 final size:29
Alignment explanation
Indices: 5814100--5814191 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
5814090 GTTACATTTT
* ** *
5814100 TTTGGCCCAATAGGGCACCACTGTAATTT
1 TTTGGCCCAATAGGGCACCTCAATAATTA
*
5814129 TTTGGCCCAATAGGGCA-CTACCATAATTA
1 TTTGGCCCAATAGGGCACCT-CAATAATTA
* *
5814158 TTTGGCCCAATAGGGTACCTCAAAAATTAA
1 TTTGGCCCAATAGGGCACCTCAATAATT-A
5814188 TTTG
1 TTTG
5814192 AGATCTACAA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
28 1 0.02
29 45 0.85
30 7 0.13
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (29 bp):
TTTGGCCCAATAGGGCACCTCAATAATTA
Found at i:5815643 original size:31 final size:29
Alignment explanation
Indices: 5815567--5815713 Score: 111
Period size: 29 Copynumber: 4.9 Consensus size: 29
5815557 GTTTGGGGAC
*
5815567 TTAGGGATGAAATTAGAATATTCAAAAGT
1 TTAGGGATGAAATTAGAATAATCAAAAGT
* * * *
5815596 TTAAGGATTAATTTAGAATGAGAATC-ATAGT
1 TTAGGGATGAAATTAGAAT---AATCAAAAGT
*
5815627 TTAGGGATGAAATTAGAATATTCAAAAGT
1 TTAGGGATGAAATTAGAATAATCAAAAGT
* * *
5815656 TTAAGGACT-AATTTAGAATGAGAATCATAA-T
1 TTAGGGA-TGAAATTAGAAT---AATCAAAAGT
* *
5815687 TTAGGGATGAAATTAAAATATTCAAAA
1 TTAGGGATGAAATTAGAATAATCAAAA
5815714 AATTTAAGGA
Statistics
Matches: 90, Mismatches: 19, Indels: 19
0.70 0.15 0.15
Matches are distributed among these distances:
28 9 0.10
29 35 0.39
30 2 0.02
31 35 0.39
32 9 0.10
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.32
Consensus pattern (29 bp):
TTAGGGATGAAATTAGAATAATCAAAAGT
Found at i:5815660 original size:60 final size:60
Alignment explanation
Indices: 5815567--5815759 Score: 309
Period size: 60 Copynumber: 3.2 Consensus size: 60
5815557 GTTTGGGGAC
5815567 TTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGATTAATTTAGAATGAGAATCATAGT
1 TTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGATTAATTTAGAATGAGAATCATAGT
* *
5815627 TTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGACTAATTTAGAATGAGAATCATAAT
1 TTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGATTAATTTAGAATGAGAATCATAGT
* * *
5815687 TTAGGGATGAAATTAAAATATTCAAAAAATTTAAGGATTAA-TT-GAATGAAAATCATAGT
1 TTAGGGATGAAATTAGAATATTC-AAAAGTTTAAGGATTAATTTAGAATGAGAATCATAGT
*
5815746 TTAAGGATGAAATT
1 TTAGGGATGAAATT
5815760 GTAAAAATTC
Statistics
Matches: 124, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
59 27 0.22
60 82 0.66
61 15 0.12
ACGTcount: A:0.46, C:0.04, G:0.18, T:0.33
Consensus pattern (60 bp):
TTAGGGATGAAATTAGAATATTCAAAAGTTTAAGGATTAATTTAGAATGAGAATCATAGT
Found at i:5815777 original size:29 final size:29
Alignment explanation
Indices: 5815684--5815777 Score: 70
Period size: 29 Copynumber: 3.2 Consensus size: 29
5815674 TGAGAATCAT
*
5815684 AATTTAGGGATGAAA-T-TAAAATATTCAAAA
1 AATTTAAGGATGAAATTGTAAAA-ATTC--AA
* * *
5815714 AATTTAAGGAT-TAATTG-AATGAAAATCAT
1 AATTTAAGGATGAAATTGTAA--AAATTCAA
*
5815743 AGTTTAAGGATGAAATTGTAAAAATTCAA
1 AATTTAAGGATGAAATTGTAAAAATTCAA
5815772 AATTTA
1 AATTTA
5815778 TTAGAGTTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 13
0.69 0.13 0.18
Matches are distributed among these distances:
29 24 0.49
30 18 0.37
31 5 0.10
32 2 0.04
ACGTcount: A:0.50, C:0.03, G:0.14, T:0.33
Consensus pattern (29 bp):
AATTTAAGGATGAAATTGTAAAAATTCAA
Found at i:5822744 original size:42 final size:42
Alignment explanation
Indices: 5822718--5822797 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 42
5822708 GCTATAGATA
*
5822718 AGTAATTTAGCGGCGTTTATGAAACAAACGCCGTAATAGAGT
1 AGTAATTTAGCGGCGTTTATGAAACAAACGACGTAATAGAGT
* * *
5822760 AGTTATTTAGCGGCGTTTGT-ATAACAAACGCCGTAATA
1 AGTAATTTAGCGGCGTTTATGA-AACAAACGACGTAATA
5822798 TGTTGTTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
41 1 0.03
42 34 0.97
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.29
Consensus pattern (42 bp):
AGTAATTTAGCGGCGTTTATGAAACAAACGACGTAATAGAGT
Found at i:5823520 original size:43 final size:42
Alignment explanation
Indices: 5823425--5823520 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 42
5823415 TGAAAGTTTG
*
5823425 GCGGTGTTTTTAAAAAAAATGTTGCAATAGGGTTACTTTATA
1 GCGGTGTTTTTAAAAAAAATGTCGCAATAGGGTTACTTTATA
** ** *
5823467 ATGGTGTTTTTACTAAAAATGTCGTAATAGGGTTAGC-TTATA
1 GCGGTGTTTTTAAAAAAAATGTCGCAATAGGGTTA-CTTTATA
5823509 GCGGTAGTTTTT
1 GCGGT-GTTTTT
5823521 TATTAAACGC
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
42 37 0.84
43 7 0.16
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.41
Consensus pattern (42 bp):
GCGGTGTTTTTAAAAAAAATGTCGCAATAGGGTTACTTTATA
Found at i:5825028 original size:22 final size:22
Alignment explanation
Indices: 5825000--5825042 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
5824990 ATGTATTTAT
*
5825000 ATGTAAATTAAGCTTATGATAA
1 ATGTAAATTAAGCTTAGGATAA
5825022 ATGTAAATTAAGCTTAGGATA
1 ATGTAAATTAAGCTTAGGATA
5825043 TATAATTACG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.44, C:0.05, G:0.16, T:0.35
Consensus pattern (22 bp):
ATGTAAATTAAGCTTAGGATAA
Found at i:5828535 original size:24 final size:25
Alignment explanation
Indices: 5828502--5828553 Score: 97
Period size: 24 Copynumber: 2.1 Consensus size: 25
5828492 AGGTGTTATT
5828502 TGAATATCACGTTTCAAATTACTAC
1 TGAATATCACGTTTCAAATTACTAC
5828527 TGAA-ATCACGTTTCAAATTACTAC
1 TGAATATCACGTTTCAAATTACTAC
5828551 TGA
1 TGA
5828554 TTATACCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.35
Consensus pattern (25 bp):
TGAATATCACGTTTCAAATTACTAC
Found at i:5832025 original size:43 final size:43
Alignment explanation
Indices: 5831953--5832264 Score: 246
Period size: 43 Copynumber: 7.4 Consensus size: 43
5831943 GTCGCAAAAC
* * * *
5831953 ATCAA-ACCTACTGCGGCGTTT-TAGCGAAAAACGCAGCTAAAC
1 ATCAACACCTATTGCGACGTTTGTA-TGAAAAACGCAGCTAAAT
* * * * *
5831995 ATCATA-ACCTATTGCGATGTTTGTCTGAAAAATGCTGGTAAAT
1 ATCA-ACACCTATTGCGACGTTTGTATGAAAAACGCAGCTAAAT
* * * *
5832038 ATTAACACCTATTGCGGCGTTTTTATGACAAACGCCA-CTAAAT
1 ATCAACACCTATTGCGACGTTTGTATGAAAAACG-CAGCTAAAT
* * *
5832081 ATCAACACCTATTGCGACGTTTGT-TGACAAATGCCGCTAAAT
1 ATCAACACCTATTGCGACGTTTGTATGAAAAACGCAGCTAAAT
* * * *
5832123 ATCAACACATATTACGACATTTGTCTGAAAAACGCTA-CTAAAT
1 ATCAACACCTATTGCGACGTTTGTATGAAAAACGC-AGCTAAAT
** * * * *
5832166 ATCAACACCTATTGCGGTGTTTTTATGACAAATGCCGCTAAAT
1 ATCAACACCTATTGCGACGTTTGTATGAAAAACGCAGCTAAAT
* * *
5832209 ATCAACACCTATTGCGGCGTTTG--T-ACAAACGCCGCTAAAT
1 ATCAACACCTATTGCGACGTTTGTATGAAAAACGCAGCTAAAT
* *
5832249 ATCAATACATATTGCG
1 ATCAACACCTATTGCG
5832265 GCATTTTTTG
Statistics
Matches: 218, Mismatches: 44, Indels: 18
0.78 0.16 0.06
Matches are distributed among these distances:
40 29 0.13
41 2 0.01
42 40 0.18
43 145 0.67
44 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (43 bp):
ATCAACACCTATTGCGACGTTTGTATGAAAAACGCAGCTAAAT
Found at i:5832103 original size:86 final size:84
Alignment explanation
Indices: 5831953--5832264 Score: 328
Period size: 86 Copynumber: 3.7 Consensus size: 84
5831943 GTCGCAAAAC
* * *
5831953 ATCAA-ACCTACTGCGGCGTTTTAGCGAAAAACG-CAGCTAAACATCATA-ACCTATTGCGATGT
1 ATCAACACCTATTGCGGCGTTTTA-TGAAAAACGCCA-CTAAATATCA-ACACCTATTGCGATGT
* * *
5832015 TTGTCTGAAAAATGCTGGTAAAT
63 TTGT-TGACAAATGCCGCTAAAT
* * *
5832038 ATTAACACCTATTGCGGCGTTTTTATGACAAACGCCACTAAATATCAACACCTATTGCGACGTTT
1 ATCAACACCTATTGCGGCG-TTTTATGAAAAACGCCACTAAATATCAACACCTATTGCGATGTTT
5832103 GTTGACAAATGCCGCTAAAT
65 GTTGACAAATGCCGCTAAAT
* * * * * * *
5832123 ATCAACACATATTACGACATTTGTCTGAAAAACGCTACTAAATATCAACACCTATTGCGGTGTTT
1 ATCAACACCTATTGCGGCGTTT-TATGAAAAACGCCACTAAATATCAACACCTATTGCGATGTTT
*
5832188 TTATGACAAATGCCGCTAAAT
65 GT-TGACAAATGCCGCTAAAT
* * * * *
5832209 ATCAACACCTATTGCGGCG-TTTGT-ACAAACGCCGCTAAATATCAATACATATTGCG
1 ATCAACACCTATTGCGGCGTTTTATGAAAAACGCCACTAAATATCAACACCTATTGCG
5832265 GCATTTTTTG
Statistics
Matches: 191, Mismatches: 30, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
83 27 0.14
84 5 0.03
85 74 0.39
86 78 0.41
87 7 0.04
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.29
Consensus pattern (84 bp):
ATCAACACCTATTGCGGCGTTTTATGAAAAACGCCACTAAATATCAACACCTATTGCGATGTTTG
TTGACAAATGCCGCTAAAT
Found at i:5832166 original size:128 final size:126
Alignment explanation
Indices: 5832014--5832270 Score: 388
Period size: 128 Copynumber: 2.0 Consensus size: 126
5832004 TATTGCGATG
* ** *
5832014 TTTGTCTGAAAAATGCTGGTAAATATTAACACCTATTGCGGCGTTTTTATGACAAACGCCACTAA
1 TTTGTCTGAAAAACGCTACTAAATATCAACACCTATTGCGGCGTTTTTATGACAAACGCCACTAA
*
5832079 ATATCAACACCTATTGCGACGTTTGTTGACAAATGCCGCTAAATATCAACACATATTACGACA
66 ATATCAACACCTATTGCGACGTTTG-T-ACAAACGCCGCTAAATATCAACACATATTACGACA
* * *
5832142 TTTGTCTGAAAAACGCTACTAAATATCAACACCTATTGCGGTGTTTTTATGACAAATGCCGCTAA
1 TTTGTCTGAAAAACGCTACTAAATATCAACACCTATTGCGGCGTTTTTATGACAAACGCCACTAA
* * * *
5832207 ATATCAACACCTATTGCGGCGTTTGTACAAACGCCGCTAAATATCAATACATATTGCGGCA
66 ATATCAACACCTATTGCGACGTTTGTACAAACGCCGCTAAATATCAACACATATTACGACA
5832268 TTT
1 TTT
5832271 TTTGTGAAAA
Statistics
Matches: 117, Mismatches: 12, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
126 34 0.29
127 1 0.01
128 82 0.70
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.30
Consensus pattern (126 bp):
TTTGTCTGAAAAACGCTACTAAATATCAACACCTATTGCGGCGTTTTTATGACAAACGCCACTAA
ATATCAACACCTATTGCGACGTTTGTACAAACGCCGCTAAATATCAACACATATTACGACA
Found at i:5834356 original size:3 final size:3
Alignment explanation
Indices: 5834348--5834378 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5834338 GGTTCAGCTC
5834348 TCT TCT TCT TCT TCT TCT TCT TCT TC- TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
5834379 CCGTGACTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:5835931 original size:23 final size:22
Alignment explanation
Indices: 5835871--5835977 Score: 60
Period size: 23 Copynumber: 4.8 Consensus size: 22
5835861 AAGTCGAGGG
* *
5835871 TTCTACGCGGTCCTTCGAGAC-A
1 TTCTACGTGGTCATTCG-GACAA
* * *
5835893 -TCTATGTGATCCTTCGGCACAA
1 TTCTACGTGGTCATTCGG-ACAA
*
5835915 TTCTACGTGGTCATTCGAGACAT
1 TTCTACGTGGTCATTCG-GACAA
* *
5835938 TTCTACGCGGTCCTTCGGGAC-A
1 TTCTACGTGGTCATTC-GGACAA
*
5835960 TTCTATGTGG-CACTTCGG
1 TTCTACGTGGTCA-TTCGG
5835978 TCCAATTTAT
Statistics
Matches: 66, Mismatches: 13, Indels: 13
0.72 0.14 0.14
Matches are distributed among these distances:
20 1 0.02
21 18 0.27
22 12 0.18
23 33 0.50
24 2 0.03
ACGTcount: A:0.18, C:0.27, G:0.23, T:0.32
Consensus pattern (22 bp):
TTCTACGTGGTCATTCGGACAA
Found at i:5837810 original size:19 final size:19
Alignment explanation
Indices: 5837786--5837838 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 19
5837776 ATTATGCCCA
5837786 ATTTTATAATAATAATAAT
1 ATTTTATAATAATAATAAT
*
5837805 ATTTTATAATAATACTAAT
1 ATTTTATAATAATAATAAT
5837824 A--TTATAATAATAATA
1 ATTTTATAATAATAATA
5837839 TTTAACGGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
17 13 0.41
19 19 0.59
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTTATAATAATAATAAT
Found at i:5838402 original size:11 final size:12
Alignment explanation
Indices: 5838383--5838412 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
5838373 TACAATACAT
5838383 ATATATTTCTTC
1 ATATATTTCTTC
5838395 ATAT-TTTCTTC
1 ATATATTTCTTC
5838406 ATATATT
1 ATATATT
5838413 ATATACATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATATTTCTTC
Found at i:5839316 original size:28 final size:28
Alignment explanation
Indices: 5839282--5839393 Score: 100
Period size: 28 Copynumber: 3.8 Consensus size: 28
5839272 CTTTTGGTAT
5839282 TCGGGTCGGTTTTTTTTAAAAATTGGGA
1 TCGGGTCGGTTTTTTTTAAAAATTGGGA
* *
5839310 TCGGGTCGGATTTTTTTTAGTTTGATATTCGGG-
1 TCGGGTCGG-TTTTTTTTA----AAAATT-GGGA
* *
5839343 TCGGGTCGGGTTTTTTTAAAAAATCGGGA
1 TCGGGTC-GGTTTTTTTTAAAAATTGGGA
* *
5839372 TCGGGTAGGCTTTTTTTAAAAA
1 TCGGGTCGGTTTTTTTTAAAAA
5839394 AATTTGGGTT
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
28 25 0.37
29 18 0.27
33 19 0.28
34 5 0.07
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.42
Consensus pattern (28 bp):
TCGGGTCGGTTTTTTTTAAAAATTGGGA
Found at i:5839613 original size:21 final size:21
Alignment explanation
Indices: 5839564--5839613 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
5839554 TAAGTTACTG
*
5839564 TTTTTATGGAATAAAAATAAT
1 TTTTTATTGAATAAAAATAAT
5839585 TTTTTATTGAATAAAAATAAT
1 TTTTTATTGAATAAAAATAAT
5839606 TTTTTATT
1 TTTTTATT
5839614 ATTTCGGGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
TTTTTATTGAATAAAAATAAT
Found at i:5840076 original size:16 final size:16
Alignment explanation
Indices: 5840047--5840082 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5840037 CCAAATATGT
5840047 TTCAGATTCCAATTCC
1 TTCAGATTCCAATTCC
* *
5840063 TTCAGTTTCTAATTCC
1 TTCAGATTCCAATTCC
5840079 TTCA
1 TTCA
5840083 CAAATTCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.06, T:0.44
Consensus pattern (16 bp):
TTCAGATTCCAATTCC
Found at i:5841166 original size:10 final size:11
Alignment explanation
Indices: 5841141--5841182 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
5841131 CATATACATG
5841141 ATATAATATAAA
1 ATATAAT-TAAA
5841153 A-ATAAATTAAA
1 ATAT-AATTAAA
*
5841164 ATATAATTAAG
1 ATATAATTAAA
5841175 ATATAATT
1 ATATAATT
5841183 TTACAATAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 21 0.78
12 6 0.22
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (11 bp):
ATATAATTAAA
Found at i:5842686 original size:18 final size:19
Alignment explanation
Indices: 5842637--5842687 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
5842627 TTTTTTAAAA
5842637 TTTAATAAAAATATTAAATT
1 TTTAATAAAAATA-TAAATT
* * *
5842657 TATAATTGAAAATA-AATTT
1 TTTAA-TAAAAATATAAATT
5842676 TTTAATAAAAAT
1 TTTAATAAAAAT
5842688 TTATTTCTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
18 6 0.24
19 8 0.32
20 4 0.16
21 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TTTAATAAAAATATAAATT
Found at i:5848058 original size:20 final size:20
Alignment explanation
Indices: 5848033--5848075 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
5848023 TCATCTGGAG
5848033 TTGTTTGATAATGAAATCAA
1 TTGTTTGATAATGAAATCAA
5848053 TTGTTTGATAATGAAATCAA
1 TTGTTTGATAATGAAATCAA
5848073 TTG
1 TTG
5848076 ACATAGACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.16, T:0.42
Consensus pattern (20 bp):
TTGTTTGATAATGAAATCAA
Found at i:5848412 original size:24 final size:24
Alignment explanation
Indices: 5848328--5848405 Score: 131
Period size: 24 Copynumber: 3.3 Consensus size: 24
5848318 TGAATTCTTT
5848328 TATGATACCTGACATGGATTCTGA
1 TATGATACCTGACATGGATTCTGA
5848352 TATGATA-CTGACATGGATTCTGA
1 TATGATACCTGACATGGATTCTGA
* *
5848375 TATGATACATGACCTGGATTCTGA
1 TATGATACCTGACATGGATTCTGA
5848399 TATGATA
1 TATGATA
5848406 TTTGACCCGA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 23 0.45
24 28 0.55
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.35
Consensus pattern (24 bp):
TATGATACCTGACATGGATTCTGA
Found at i:5849941 original size:27 final size:26
Alignment explanation
Indices: 5849911--5849997 Score: 88
Period size: 26 Copynumber: 3.2 Consensus size: 26
5849901 ATATAAAGGA
5849911 AAAAATGAAGATAAATAAAAATAAAAG
1 AAAAATGAA-ATAAATAAAAATAAAAG
*
5849938 AAAAAGGAAATAAA-ATAAAATAAAAG
1 AAAAATGAAATAAATA-AAAATAAAAG
* *
5849964 TAAAAATG-TATAAATATAAATAAAATAG
1 -AAAAATGAAATAAATAAAAAT-AAA-AG
5849992 AAAAAT
1 AAAAAT
5849998 AATTGTAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
25 1 0.02
26 24 0.47
27 24 0.47
28 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.09, T:0.18
Consensus pattern (26 bp):
AAAAATGAAATAAATAAAAATAAAAG
Found at i:5849950 original size:26 final size:27
Alignment explanation
Indices: 5849911--5849988 Score: 90
Period size: 26 Copynumber: 2.9 Consensus size: 27
5849901 ATATAAAGGA
5849911 AAAAATGAAGATAAATAAAAATAAAAG-
1 AAAAATGAA-ATAAATAAAAATAAAAGT
*
5849938 AAAAAGGAAATAAA-ATAAAATAAAAGT
1 AAAAATGAAATAAATA-AAAATAAAAGT
* *
5849965 AAAAATG-TATAAATATAAATAAAA
1 AAAAATGAAATAAATAAAAATAAAA
5849989 TAGAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
25 1 0.02
26 28 0.64
27 15 0.34
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (27 bp):
AAAAATGAAATAAATAAAAATAAAAGT
Found at i:5850346 original size:3 final size:3
Alignment explanation
Indices: 5850333--5850370 Score: 51
Period size: 3 Copynumber: 12.3 Consensus size: 3
5850323 TTTGAAATCG
5850333 AAT AA- AAT AAT AAT AAT AAT AAT ATAT AAT AAAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT -AAT AAT A
5850371 CATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 2 0.06
3 24 0.75
4 6 0.19
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5850391 original size:25 final size:23
Alignment explanation
Indices: 5850341--5850395 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
5850331 CGAATAAAAT
5850341 AATAATAATAATAATATATAATA
1 AATAATAATAATAATATATAATA
*
5850364 AATAATACAT-ATATATACTATATTA
1 AATAATA-ATAATA-ATA-TATAATA
5850389 AATAATA
1 AATAATA
5850396 TAAACATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 10 0.36
24 5 0.18
25 13 0.46
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (23 bp):
AATAATAATAATAATATATAATA
Found at i:5851553 original size:18 final size:17
Alignment explanation
Indices: 5851530--5851577 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
5851520 AATATGTGTA
*
5851530 AAATATATGTAATAAAAT
1 AAATATATCT-ATAAAAT
*
5851548 AAATATAATCTATAATAT
1 AAATAT-ATCTATAAAAT
5851566 AAATATAT-TATA
1 AAATATATCTATA
5851578 TTAAAGGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 4 0.15
17 2 0.07
18 18 0.67
19 3 0.11
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATATATCTATAAAAT
Found at i:5852534 original size:106 final size:106
Alignment explanation
Indices: 5852404--5852595 Score: 330
Period size: 106 Copynumber: 1.8 Consensus size: 106
5852394 ACAGCCAACC
*
5852404 GCCCCTTCGCTGTGAAGTTAAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAA
1 GCCCCTTCGCTGTGAAGTTAAGCTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAA
5852469 ATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAATCAGTT
66 ATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAATCAGTT
* * * *
5852510 GCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAA
1 GCCCCTTCGCTGTGAAGTTAAGCTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAA
*
5852575 ATTGGCTCTGAAACTGGGAAG
66 ATTGACTCTGAAACTGGGAAG
5852596 CCCCTTTGTC
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
106 80 1.00
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (106 bp):
GCCCCTTCGCTGTGAAGTTAAGCTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAA
ATTGACTCTGAAACTGGGAAGTTGTTTGTTGACAATCAGTT
Found at i:5856466 original size:22 final size:23
Alignment explanation
Indices: 5856441--5856484 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
5856431 AATTAAGTTT
5856441 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
5856463 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
5856485 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:5862416 original size:20 final size:19
Alignment explanation
Indices: 5862389--5862449 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
5862379 CATTTTGGTG
5862389 CAGAGGGAATCGATACCCC
1 CAGAGGGAATCGATACCCC
* *
5862408 CATGAGGGAACCGATTCCCCC
1 CA-GAGGGAATCGA-TACCCC
*
5862429 CACAGGGGAATCGATACCCC
1 CAGA-GGGAATCGATACCCC
5862449 C
1 C
5862450 CTGGGGTTCT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
19 2 0.06
20 17 0.50
21 15 0.44
ACGTcount: A:0.28, C:0.36, G:0.25, T:0.11
Consensus pattern (19 bp):
CAGAGGGAATCGATACCCC
Found at i:5873570 original size:5 final size:4
Alignment explanation
Indices: 5873529--5873655 Score: 50
Period size: 4 Copynumber: 30.8 Consensus size: 4
5873519 AAGATACATG
* *
5873529 AAAT AAAT AAAT AAAAGT AAAGT AAAA AAAT GAAT AAGAT AAAT AAAT
1 AAAT AAAT AAAT -AAA-T AAA-T AAAT AAAT AAAT AA-AT AAAT AAAT
* * *
5873577 AAAAT GAAAT -AAT -AAT -AAT AATGT ATAC ACAAT AAAT AAAT AAA-
1 -AAAT -AAAT AAAT AAAT AAAT AA-AT AAAT A-AAT AAAT AAAT AAAT
* * *
5873621 AATT AGAAG AAA- ATAA- AAAT AAAT AAAT ACAT AAA
1 AAAT A-AAT AAAT A-AAT AAAT AAAT AAAT AAAT AAA
5873656 ACAAATATAA
Statistics
Matches: 96, Mismatches: 16, Indels: 22
0.72 0.12 0.16
Matches are distributed among these distances:
3 14 0.15
4 52 0.54
5 29 0.30
6 1 0.01
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:5873588 original size:10 final size:9
Alignment explanation
Indices: 5873529--5873594 Score: 50
Period size: 9 Copynumber: 7.2 Consensus size: 9
5873519 AAGATACATG
5873529 AAAT-AAAT
1 AAATAAAAT
5873537 AAATAAAAGT
1 AAATAAAA-T
5873547 AAAGTAAAA-
1 AAA-TAAAAT
*
5873556 AAAT-GAAT
1 AAATAAAAT
5873564 AAGAT-AAAT
1 AA-ATAAAAT
5873573 AAATAAAAT
1 AAATAAAAT
5873582 GAAATAATAAT
1 -AAATAA-AAT
5873593 AA
1 AA
5873595 TAATGTATAC
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
7 2 0.04
8 9 0.19
9 17 0.35
10 12 0.25
11 8 0.17
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5873712 original size:21 final size:22
Alignment explanation
Indices: 5873683--5873723 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5873673 AAATGAACAT
5873683 AAATAAAAATAAAAGGAAAAGG
1 AAATAAAAATAAAAGGAAAAGG
*
5873705 AAAT-AAAATAAAAGTAAAA
1 AAATAAAAATAAAAGGAAAA
5873724 ATGTATAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (22 bp):
AAATAAAAATAAAAGGAAAAGG
Found at i:5873999 original size:2 final size:2
Alignment explanation
Indices: 5873992--5874046 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
5873982 GGCCCGCATA
5873992 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5874034 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
5874047 AATGATATAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5874148 original size:9 final size:9
Alignment explanation
Indices: 5874134--5874167 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
5874124 CGAATAAAAT
5874134 AATAATAAA
1 AATAATAAA
5874143 AATAATAAA
1 AATAATAAA
5874152 AAT-ATAATA
1 AATAATAA-A
5874161 AATAATA
1 AATAATA
5874168 TATATATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.17
9 16 0.70
10 3 0.13
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (9 bp):
AATAATAAA
Found at i:5881284 original size:22 final size:21
Alignment explanation
Indices: 5881255--5881296 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5881245 AAATTATATC
5881255 TAAAGTTTAGA-ATTTTTTTAA
1 TAAAGTTTA-ATATTTTTTTAA
5881276 TAAATGTTTAATATTTTTTTA
1 TAAA-GTTTAATATTTTTTTA
5881297 TTACAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (21 bp):
TAAAGTTTAATATTTTTTTAA
Found at i:5881727 original size:59 final size:59
Alignment explanation
Indices: 5881656--5881808 Score: 134
Period size: 60 Copynumber: 2.6 Consensus size: 59
5881646 TACTTGGTCT
** * * *
5881656 TTAAA-TTATTGAATATTTTAATTTTATCC-CTAAATTATGA-TTTCATTCTAAATTAATC
1 TTAAACTT-TTGAATATTCCAATTTCATCCTC-AAACTATGACTCTCATTCTAAATTAATC
* * * *
5881714 ATTAAACTTTTGAACATTCCAATTTCATTCTCAAACTATGACTCTCATTTTAAATTAGTC
1 -TTAAACTTTTGAATATTCCAATTTCATCCTCAAACTATGACTCTCATTCTAAATTAATC
* *
5881774 TCTAAACTTTTGAAT-TTGCCAATATCATCCCCAAA
1 T-TAAACTTTTGAATATT-CCAATTTCATCCTCAAA
5881809 TTCGTCCAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
59 32 0.42
60 44 0.58
ACGTcount: A:0.35, C:0.18, G:0.05, T:0.43
Consensus pattern (59 bp):
TTAAACTTTTGAATATTCCAATTTCATCCTCAAACTATGACTCTCATTCTAAATTAATC
Found at i:5883298 original size:22 final size:22
Alignment explanation
Indices: 5883270--5883315 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5883260 ACTGGTTATT
* *
5883270 ATATATATTATTTTTATCATGA
1 ATATATATGATGTTTATCATGA
*
5883292 ATATATATGATGTTTATTATGA
1 ATATATATGATGTTTATCATGA
5883314 AT
1 AT
5883316 GTTACTTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.52
Consensus pattern (22 bp):
ATATATATGATGTTTATCATGA
Found at i:5883610 original size:61 final size:61
Alignment explanation
Indices: 5883504--5883621 Score: 155
Period size: 61 Copynumber: 1.9 Consensus size: 61
5883494 GTAGGTAGAG
* * * * * *
5883504 GGCACAACCTTATGTGTCGCATCTGGATTAGCACTAGTGTATAAACCTAGTGTAGGTGATA
1 GGCACAACCTTATGTGTCACATCCGGAATAGCACTAGAGCATAAACCTAGTGCAGGTGATA
* * *
5883565 GGCACAACCTTATGTGTCATATCCGGAATAGCACTAGAGCGTAAACTTAGTGCAGGT
1 GGCACAACCTTATGTGTCACATCCGGAATAGCACTAGAGCATAAACCTAGTGCAGGT
5883622 TTAGCACTAC
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (61 bp):
GGCACAACCTTATGTGTCACATCCGGAATAGCACTAGAGCATAAACCTAGTGCAGGTGATA
Found at i:5884536 original size:17 final size:16
Alignment explanation
Indices: 5884503--5884532 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5884493 CTTATAAAGG
5884503 TGAAAAATATAGTGTA
1 TGAAAAATATAGTGTA
5884519 TGAAAAATAT-GTGT
1 TGAAAAATATAGTGT
5884533 GTATTTGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (16 bp):
TGAAAAATATAGTGTA
Found at i:5889905 original size:22 final size:22
Alignment explanation
Indices: 5889860--5889905 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
5889850 ATTGGTTATT
* *
5889860 ATATATATGATTTTTATCATGA
1 ATATATATGATGTTTATCACGA
*
5889882 ATATATATGATGTTTATTACGA
1 ATATATATGATGTTTATCACGA
5889904 AT
1 AT
5889906 GTTTCTTCGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (22 bp):
ATATATATGATGTTTATCACGA
Found at i:5893583 original size:21 final size:21
Alignment explanation
Indices: 5893557--5893608 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
5893547 TATGTTATGA
5893557 GAATGTGAACTTTGAATA-AGT
1 GAATGTGAACTTTGAA-ACAGT
5893578 GAATGTGAACTTTGAAACAGT
1 GAATGTGAACTTTGAAACAGT
*
5893599 GAAAGTGAAC
1 GAATGTGAAC
5893609 AAACTCTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.40, C:0.08, G:0.25, T:0.27
Consensus pattern (21 bp):
GAATGTGAACTTTGAAACAGT
Found at i:5893820 original size:21 final size:21
Alignment explanation
Indices: 5893741--5893821 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
5893731 GTCGAGGGTC
* *
5893741 TTATGTGGTCCTCCGGGATAA
1 TTATGTGGTACTTCGGGATAA
* * *
5893762 ATATGTGGCACTTCGATG-TAAA
1 TTATGTGGTACTTCG-GGAT-AA
*
5893784 CCTATGTGGT-CTTTCGGGATAA
1 -TTATGTGGTAC-TTCGGGATAA
5893806 TTATGTGGTACTTCGG
1 TTATGTGGTACTTCGG
5893822 TGCAAATTAC
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
21 25 0.56
22 8 0.18
23 12 0.27
ACGTcount: A:0.21, C:0.16, G:0.27, T:0.36
Consensus pattern (21 bp):
TTATGTGGTACTTCGGGATAA
Found at i:5894271 original size:26 final size:26
Alignment explanation
Indices: 5894232--5894293 Score: 106
Period size: 26 Copynumber: 2.4 Consensus size: 26
5894222 CTGGTCAATT
* *
5894232 TTGTAAACTTACATATATTTTGTATG
1 TTGTAAACTCACATATATTTTGTATA
5894258 TTGTAAACTCACATATATTTTGTATA
1 TTGTAAACTCACATATATTTTGTATA
5894284 TTGTAAACTC
1 TTGTAAACTC
5894294 TTACTTTTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.32, C:0.11, G:0.10, T:0.47
Consensus pattern (26 bp):
TTGTAAACTCACATATATTTTGTATA
Found at i:5896562 original size:22 final size:22
Alignment explanation
Indices: 5896537--5896578 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5896527 ATTTTTAAAA
5896537 AATGAAATCAAAATCAAAATCG
1 AATGAAATCAAAATCAAAATCG
* *
5896559 AATGATATGAAAATCAAAAT
1 AATGAAATCAAAATCAAAAT
5896579 TTTCGATTCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.10, G:0.10, T:0.21
Consensus pattern (22 bp):
AATGAAATCAAAATCAAAATCG
Found at i:5897100 original size:25 final size:23
Alignment explanation
Indices: 5897072--5897118 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 23
5897062 AGAAACTAAC
5897072 TTATAAAATTTTAGAGATAATAAAT
1 TTATAAAATTTTA-AGAT-ATAAAT
5897097 TTATAAAATTTTAAGATATAAA
1 TTATAAAATTTTAAGATATAAA
5897119 AATATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.23
24 4 0.18
25 13 0.59
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.40
Consensus pattern (23 bp):
TTATAAAATTTTAAGATATAAAT
Found at i:5897133 original size:17 final size:17
Alignment explanation
Indices: 5897092--5897138 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
5897082 TTAGAGATAA
5897092 TAAATT-TATAAAATTT
1 TAAATTATATAAAATTT
5897108 TAAGA-TATA-AAAATATT
1 TAA-ATTATATAAAAT-TT
5897125 TAAATTATATAAAA
1 TAAATTATATAAAA
5897139 AAATTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
16 10 0.38
17 12 0.46
18 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TAAATTATATAAAATTT
Found at i:5897136 original size:19 final size:19
Alignment explanation
Indices: 5897112--5897149 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
5897102 AAATTTTAAG
* *
5897112 ATATAAAAATATTTAAATT
1 ATATAAAAAAATTAAAATT
5897131 ATATAAAAAAATTAAAATT
1 ATATAAAAAAATTAAAATT
5897150 TTCAAGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (19 bp):
ATATAAAAAAATTAAAATT
Found at i:5897432 original size:28 final size:28
Alignment explanation
Indices: 5897393--5897455 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
5897383 TTATATGGAA
* *
5897393 AAAAATATTTTAGGTATCTA-TTTAACC
1 AAAAATACTTTAGGTATATATTTTAACC
5897420 AAATAATACTTTAGGTATATATTTTAACC
1 AAA-AATACTTTAGGTATATATTTTAACC
5897449 AAAAATA
1 AAAAATA
5897456 TAAATTTAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
27 3 0.09
28 19 0.59
29 10 0.31
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (28 bp):
AAAAATACTTTAGGTATATATTTTAACC
Found at i:5897464 original size:31 final size:28
Alignment explanation
Indices: 5897392--5897464 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
5897382 CTTATATGGA
* *
5897392 AAAAAATATTTTAGGTATCTATTTAACC
1 AAAAAATAATTTAGGTATATATTTAACC
* *
5897420 AAATAATACTTTAGGTATATATTTTAACC
1 AAAAAATAATTTAGGTATATA-TTTAACC
5897449 AAAAATATAAATTTAG
1 AAAAA-AT-AATTTAG
5897465 ATACTTATGT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 18 0.49
29 11 0.30
30 2 0.05
31 6 0.16
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (28 bp):
AAAAAATAATTTAGGTATATATTTAACC
Found at i:5897522 original size:30 final size:30
Alignment explanation
Indices: 5897485--5897560 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
5897475 TGATTAAAAA
*
5897485 ATACTTTAGGTACTTAGATGAAAAAATGAT
1 ATACTTTAGGTACTTAAATGAAAAAATGAT
* *
5897515 GTACTTTAGGTACTTAAATGAAAAACTGAT
1 ATACTTTAGGTACTTAAATGAAAAAATGAT
*
5897545 ATACTTTATGTACTTA
1 ATACTTTAGGTACTTA
5897561 TTTTTAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.37
Consensus pattern (30 bp):
ATACTTTAGGTACTTAAATGAAAAAATGAT
Found at i:5898050 original size:24 final size:25
Alignment explanation
Indices: 5897993--5898051 Score: 77
Period size: 24 Copynumber: 2.4 Consensus size: 25
5897983 TTTTATAAAA
*
5897993 TATATATTTTAAAATTATTTGATTT
1 TATATATTTTAAAATTATATGATTT
* *
5898018 AAAAT-TTTTAAAA-TATATGATTT
1 TATATATTTTAAAATTATATGATTT
5898041 TATATATTTTA
1 TATATATTTTA
5898052 TTAATAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
23 12 0.43
24 13 0.46
25 3 0.11
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
TATATATTTTAAAATTATATGATTT
Found at i:5898060 original size:39 final size:41
Alignment explanation
Indices: 5897966--5898061 Score: 103
Period size: 39 Copynumber: 2.4 Consensus size: 41
5897956 TAATCGTGAC
* *
5897966 TATTTTAAATAATCAAATTTTATAAAATATATATTTTAAAAT
1 TATTTT-ATTAATAAAATTTTATAAAATATATATTTTAAAAT
* *
5898008 TATTTGATT--TAAAATTTT-TAAAATATATGATTTT-ATA-
1 TATTTTATTAATAAAATTTTATAAAATATAT-ATTTTAAAAT
5898045 TATTTTATTAATAAAAT
1 TATTTTATTAATAAAAT
5898062 AAATTTAAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
37 8 0.17
38 12 0.26
39 19 0.41
41 2 0.04
42 5 0.11
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (41 bp):
TATTTTATTAATAAAATTTTATAAAATATATATTTTAAAAT
Found at i:5904416 original size:21 final size:21
Alignment explanation
Indices: 5904367--5904417 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
5904357 AATTATGTGA
*
5904367 TAGGGTTTAAGGTTTAGAGTT
1 TAGGGTTTAAGGTCTAGAGTT
** *
5904388 TAAAGTTTAGGGTCTAGAGTT
1 TAGGGTTTAAGGTCTAGAGTT
5904409 TAGGGTTTA
1 TAGGGTTTA
5904418 TGATTTAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.02, G:0.31, T:0.41
Consensus pattern (21 bp):
TAGGGTTTAAGGTCTAGAGTT
Found at i:5905819 original size:11 final size:11
Alignment explanation
Indices: 5905803--5905861 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
5905793 GCTCAAAATT
*
5905803 GAGTTTGAATC
1 GAGTTTCAATC
5905814 GAGTTTCAATC
1 GAGTTTCAATC
*
5905825 GAG-CTCAGAATC
1 GAGTTTC--AATC
5905837 GAGTTTCAATC
1 GAGTTTCAATC
5905848 GAGCTTT-AATC
1 GAG-TTTCAATC
5905859 GAG
1 GAG
5905862 CTCTTAATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
10 2 0.05
11 27 0.66
12 10 0.24
13 2 0.05
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (11 bp):
GAGTTTCAATC
Found at i:5905828 original size:34 final size:34
Alignment explanation
Indices: 5905778--5905864 Score: 113
Period size: 34 Copynumber: 2.6 Consensus size: 34
5905768 TAGGGGCAAT
* * * *
5905778 TCGAGCTTGAAACGAGCTCAAAATTGAGTTTGAA
1 TCGAGCTTTAATCGAGCTCAAAATCGAGTTTCAA
*
5905812 TCGAG-TTTCAATCGAGCTCAGAATCGAGTTTCAA
1 TCGAGCTTT-AATCGAGCTCAAAATCGAGTTTCAA
5905846 TCGAGCTTTAATCGAGCTC
1 TCGAGCTTTAATCGAGCTC
5905865 TTAATTTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 2 0.04
34 41 0.89
35 3 0.07
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (34 bp):
TCGAGCTTTAATCGAGCTCAAAATCGAGTTTCAA
Found at i:5905835 original size:23 final size:23
Alignment explanation
Indices: 5905809--5905852 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
5905799 AATTGAGTTT
5905809 GAATCGAGTTTCAATCGAGCTCA
1 GAATCGAGTTTCAATCGAGCTCA
5905832 GAATCGAGTTTCAATCGAGCT
1 GAATCGAGTTTCAATCGAGCT
5905853 TTAATCGAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (23 bp):
GAATCGAGTTTCAATCGAGCTCA
Found at i:5905862 original size:11 final size:11
Alignment explanation
Indices: 5905810--5905869 Score: 52
Period size: 11 Copynumber: 5.3 Consensus size: 11
5905800 ATTGAGTTTG
5905810 AATCGAG-TTT
1 AATCGAGCTTT
**
5905820 CAATCGAGCTCAG
1 -AATCGAGCT-TT
5905833 AATCGAG-TTT
1 AATCGAGCTTT
5905843 CAATCGAGCTTT
1 -AATCGAGCTTT
5905855 AATCGAGCTCTT
1 AATCGAGCT-TT
5905867 AAT
1 AAT
5905870 TTTTTTTGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
11 24 0.60
12 16 0.40
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (11 bp):
AATCGAGCTTT
Found at i:5906792 original size:11 final size:11
Alignment explanation
Indices: 5906776--5906800 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
5906766 TTTCCCCTCA
5906776 AAATAAAATAG
1 AAATAAAATAG
5906787 AAATAAAATAG
1 AAATAAAATAG
5906798 AAA
1 AAA
5906801 AAACCCCTTT
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:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (11 bp):
AAATAAAATAG
Found at i:5914288 original size:22 final size:22
Alignment explanation
Indices: 5914261--5914307 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
5914251 TGTCCAATGA
5914261 GAGGGGTGTGACCGGCAATAAT
1 GAGGGGTGTGACCGGCAATAAT
*
5914283 GAGGGGTGTGACCGGCAATTAT
1 GAGGGGTGTGACCGGCAATAAT
5914305 GAG
1 GAG
5914308 TTCCATCGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.13, G:0.43, T:0.19
Consensus pattern (22 bp):
GAGGGGTGTGACCGGCAATAAT
Found at i:5915228 original size:216 final size:210
Alignment explanation
Indices: 5914850--5915656 Score: 1202
Period size: 216 Copynumber: 3.8 Consensus size: 210
5914840 ATTTAAGAAT
5914850 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA-A---A--AG
*
5914915 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAA-TACTGAATTATAC
60 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * * * * *
5914979 CCATTTAAAAAGTTATGGGCCAATTAAAAAAATAGAATTAAGTAATAAGTATAGATCAATTTCAT
125 TCATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAG
5915044 ATGCAAATAAAATTTGGAGGAC
189 ATGCAAATAAAATTTGGAGGAC
5915066 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA-A---A--AG
* *
5915131 GGATCAAATCGAAATAATTTTAAATTGTGATGCTGAAATTAATACAAAAAAGTACTAAATTATAC
60 GGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATAC
*
5915196 TCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTAAGA
125 TCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGA
5915261 TGCAAATAAAATTTGGAGGAC
190 TGCAAATAAAATTTGGAGGAC
*
5915282 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATATATTAAACAACACAAAAGGGATCA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAAAAGGGATCA
* * *
5915347 AATTGAAATAATTTAAAATTTTGAGGTT-AAATTAATACAAAAAAGTACTAAATTATAC-CTATT
66 AATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACTC-ATT
*
5915410 TAAAAAGTTAT--G----TTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGGTGCAA
130 TAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAA
5915469 ATAAAATTTGGAGGAC
195 ATAAAATTTGGAGGAC
* * * *
5915485 TAAATTGAATAAATATGAAATTACAAATAAAAATTT-AATATATTAAACAACACAAAAAGGATTA
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAAAAGGGATCA
* *
5915549 AATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAATGTACTAAATTATACTCATTT
66 AATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACTCATTT
* * *
5915614 AAAAAGTTATGGGCCAATTGATAAATATAAATAAGTAATAAGT
131 AAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGT
5915657 TGAGGAAAAA
Statistics
Matches: 554, Mismatches: 27, Indels: 27
0.91 0.04 0.04
Matches are distributed among these distances:
202 52 0.09
203 139 0.25
204 1 0.00
205 1 0.00
207 1 0.00
208 1 0.00
209 67 0.12
210 31 0.06
212 1 0.00
215 1 0.00
216 223 0.40
217 36 0.06
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (210 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACAAAAGGGATCA
AATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATACTCATTT
AAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCAGATGCAAA
TAAAATTTGGAGGAC
Found at i:5915702 original size:16 final size:17
Alignment explanation
Indices: 5915681--5915792 Score: 68
Period size: 18 Copynumber: 6.4 Consensus size: 17
5915671 AAAACAACTA
5915681 ATATATATATATATA-T
1 ATATATATATATATACT
*
5915697 ATATATATAATATACACT
1 ATATATAT-ATATATACT
* * *
5915715 ATATAGTTTATATAAAGT
1 ATATA-TATATATATACT
*
5915733 ATATATTATATATAAAACT
1 ATATA-TATATAT-ATACT
*
5915752 ATAGT-T-TATATATATT
1 ATA-TATATATATATACT
* * *
5915768 ATGTATAAAGTATAAACT
1 ATATATATA-TATATACT
5915786 ATATATA
1 ATATATA
5915793 CCATGTATAA
Statistics
Matches: 74, Mismatches: 14, Indels: 14
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.01
16 14 0.19
17 12 0.16
18 37 0.50
19 9 0.12
20 1 0.01
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (17 bp):
ATATATATATATATACT
Found at i:5915766 original size:2 final size:2
Alignment explanation
Indices: 5915681--5915746 Score: 64
Period size: 2 Copynumber: 32.5 Consensus size: 2
5915671 AAAACAACTA
* *
5915681 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AC ACT AT AT AGT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT
*
5915724 AT AT AA AGT AT AT AT -T AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT A
5915747 AAACTATAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
1 2 0.04
2 48 0.91
3 3 0.06
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5915789 original size:27 final size:28
Alignment explanation
Indices: 5915732--5915822 Score: 87
Period size: 27 Copynumber: 3.2 Consensus size: 28
5915722 TTATATAAAG
* * * *
5915732 TATATATTATATATAAAACTATAGT-TTA
1 TATATATCATGTAT-AAACTATAATACTA
* *
5915760 TATATATTATGTATAAAGTATAA-ACTA
1 TATATATCATGTATAAACTATAATACTA
*
5915787 TATATACCATGTATAAACTATAATACTA
1 TATATATCATGTATAAACTATAATACTA
5915815 TAGTATAT
1 TA-TATAT
5915823 GAACTATTGA
Statistics
Matches: 52, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 29 0.56
28 19 0.37
29 4 0.08
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (28 bp):
TATATATCATGTATAAACTATAATACTA
Found at i:5915820 original size:20 final size:21
Alignment explanation
Indices: 5915776--5915821 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
5915766 TTATGTATAA
5915776 AGTATAAACTATATATACCAT
1 AGTATAAACTATATATACCAT
*
5915797 -GTATAAACTATA-ATACTAT
1 AGTATAAACTATATATACCAT
5915816 AGTATA
1 AGTATA
5915822 TGAACTATTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.35
Consensus pattern (21 bp):
AGTATAAACTATATATACCAT
Found at i:5915970 original size:26 final size:25
Alignment explanation
Indices: 5915927--5915983 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 25
5915917 TTGTATAAAT
*
5915927 TATATAGTTTATTAATATAATATATA
1 TATATAGTTTAGTAATAT-ATATATA
* *
5915953 TATATAGTTTAGGT-ATATTTATATT
1 TATATAGTTTA-GTAATATATATATA
5915978 TATATA
1 TATATA
5915984 AACTACATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 11 0.41
26 15 0.56
27 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (25 bp):
TATATAGTTTAGTAATATATATATA
Found at i:5916107 original size:24 final size:24
Alignment explanation
Indices: 5916080--5916155 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 24
5916070 ATATATAAAT
*
5916080 TATATAGTTTACATATGACCTGTA
1 TATATAGTTTACATATGACCTATA
** *
5916104 TATATA---TACTATAGTTGATATTTA
1 TATATAGTTTAC-ATA--TGACCTATA
5916128 TATATAGTTTACATATGACCTATA
1 TATATAGTTTACATATGACCTATA
5916152 TATA
1 TATA
5916156 CTATAGTTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
21 3 0.08
22 3 0.08
24 28 0.70
26 3 0.08
27 3 0.08
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (24 bp):
TATATAGTTTACATATGACCTATA
Found at i:5916132 original size:22 final size:21
Alignment explanation
Indices: 5916104--5916219 Score: 67
Period size: 22 Copynumber: 5.3 Consensus size: 21
5916094 ATGACCTGTA
5916104 TATATATACTATAGTTGATATT
1 TATATATACTATAGTT-ATATT
* * ** **
5916126 TATATATAGTTTACATATGACC
1 TATATATACTATAGTTAT-ATT
5916148 TATATATACTATAGTTATATT
1 TATATATACTATAGTTATATT
*
5916169 TATACTATA-TATTA-TATATATAC
1 TATA-TATACTA-TAGT-TATAT-T
*
5916192 TATATATACCATAG-TATAATT
1 TATATATACTATAGTTAT-ATT
*
5916213 TACATAT
1 TATATAT
5916220 GAACTATATA
Statistics
Matches: 70, Mismatches: 16, Indels: 17
0.68 0.16 0.17
Matches are distributed among these distances:
21 19 0.27
22 46 0.66
23 5 0.07
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (21 bp):
TATATATACTATAGTTATATT
Found at i:5916134 original size:48 final size:43
Alignment explanation
Indices: 5916080--5916219 Score: 142
Period size: 44 Copynumber: 3.1 Consensus size: 43
5916070 ATATATAAAT
5916080 TATATAGTTTACATATGACCTGTATATATATACTATAGTTGATATTTA
1 TATATAGTTTACATATGACC----TATATATACTATAGTT-ATATTTA
5916128 TATATAGTTTACATATGACCTATATATACTATAGTTATATTTA
1 TATATAGTTTACATATGACCTATATATACTATAGTTATATTTA
* * *
5916171 TACTATA-TATTATATAT-ATACTATATATACCATAG-TATAATTTA
1 TA-TATAGT-TTACATATGA-CCTATATATACTATAGTTAT-ATTTA
*
5916215 CATAT
1 TATAT
5916220 GAACTATATA
Statistics
Matches: 84, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
43 17 0.20
44 47 0.56
48 20 0.24
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (43 bp):
TATATAGTTTACATATGACCTATATATACTATAGTTATATTTA
Found at i:5916159 original size:9 final size:9
Alignment explanation
Indices: 5916147--5916200 Score: 60
Period size: 9 Copynumber: 6.1 Consensus size: 9
5916137 TACATATGAC
5916147 CTATATATA
1 CTATATATA
5916156 CTATAGT-TA
1 CTATA-TATA
*
5916165 -TATTTATA
1 CTATATATA
5916173 CTATATATTA
1 CTATATA-TA
5916183 -TATATATA
1 CTATATATA
5916191 CTATATATA
1 CTATATATA
5916200 C
1 C
5916201 CATAGTATAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
7 1 0.03
8 7 0.18
9 27 0.71
10 3 0.08
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (9 bp):
CTATATATA
Found at i:5916185 original size:18 final size:18
Alignment explanation
Indices: 5916148--5916198 Score: 77
Period size: 18 Copynumber: 2.9 Consensus size: 18
5916138 ACATATGACC
*
5916148 TATATATACTATA-GTTA
1 TATATATACTATATATTA
*
5916165 TATTTATACTATATATTA
1 TATATATACTATATATTA
5916183 TATATATACTATATAT
1 TATATATACTATATAT
5916199 ACCATAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (18 bp):
TATATATACTATATATTA
Found at i:5916348 original size:51 final size:52
Alignment explanation
Indices: 5916291--5916475 Score: 220
Period size: 51 Copynumber: 3.5 Consensus size: 52
5916281 AACTATATAA
*
5916291 TATATATAGACTATATGGTATATATAAACTATACATTA-TATATAGTTCATTAG
1 TATATATA-ACTATATAGTATATATAAAC-ATACATTATTATATAGTTCATTAG
*
5916344 TATATATTAACTATATAGAATATATAAAC-TACA-TATTATATAGTTCATTAG
1 TATATA-TAACTATATAGTATATATAAACATACATTATTATATAGTTCATTAG
*
5916395 TATATATAACCTATATAGTATATGATATATACAAACTATATATTATATAGTTCATTAG
1 TATATATAA-CTATATAGTATAT-ATA-A-ACATAC-AT-TATTATATAGTTCATTAG
5916453 TATATA-AAC--TATAGTATATATAA
1 TATATATAACTATATAGTATATATAA
5916476 CTATATTAAT
Statistics
Matches: 118, Mismatches: 4, Indels: 21
0.83 0.03 0.15
Matches are distributed among these distances:
50 5 0.04
51 37 0.31
52 4 0.03
53 28 0.24
54 14 0.12
55 2 0.02
56 2 0.02
57 2 0.02
58 24 0.20
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (52 bp):
TATATATAACTATATAGTATATATAAACATACATTATTATATAGTTCATTAG
Found at i:5916384 original size:71 final size:69
Alignment explanation
Indices: 5916246--5916385 Score: 192
Period size: 71 Copynumber: 2.0 Consensus size: 69
5916236 CCCTAAACCC
* * * *
5916246 TAAACTATACATTATATAGTTTATTAGTATATATAAACTATATAATATATATAGACTATATGGTA
1 TAAACTATACATTATATAGTTCATTAGTATATATAAACTATATAATATATATAAACTACATAGTA
5916311 TATA
66 TATA
*
5916315 TAAACTATACATTATATATAGTTCATTAGTATATATTAACTATATAGA-ATATATAAACTACATA
1 TAAACTATACA-T-TATATAGTTCATTAGTATATATAAACTATATA-ATATATATAAACTACATA
*
5916379 TTATATA
63 GTATATA
5916386 GTTCATTAGT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
69 11 0.18
70 1 0.02
71 49 0.79
72 1 0.02
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (69 bp):
TAAACTATACATTATATAGTTCATTAGTATATATAAACTATATAATATATATAAACTACATAGTA
TATA
Found at i:5916415 original size:18 final size:18
Alignment explanation
Indices: 5916270--5916417 Score: 119
Period size: 18 Copynumber: 8.4 Consensus size: 18
5916260 TATAGTTTAT
5916270 TAGTATATATAAACTATA
1 TAGTATATATAAACTATA
* *
5916288 TAATATATATAGACTATA
1 TAGTATATATAAACTATA
*
5916306 TGGTATATATAAACTATA
1 TAGTATATATAAACTATA
* * **
5916324 CATTATATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
*
5916341 TAGTATATATTAACTATA
1 TAGTATATATAAACTATA
* *
5916359 TAGAATATATAAACTACA
1 TAGTATATATAAACTATA
**
5916377 TA-T-TATAT-AGTTCAT-
1 TAGTATATATAAACT-ATA
*
5916392 TAGTATATATAACCTATA
1 TAGTATATATAAACTATA
5916410 TAGTATAT
1 TAGTATAT
5916418 GATATATACA
Statistics
Matches: 99, Mismatches: 23, Indels: 16
0.72 0.17 0.12
Matches are distributed among these distances:
15 4 0.04
16 7 0.07
17 19 0.19
18 69 0.70
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (18 bp):
TAGTATATATAAACTATA
Found at i:5916469 original size:14 final size:15
Alignment explanation
Indices: 5916450--5916480 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5916440 TATAGTTCAT
5916450 TAGTATATA-AACTA
1 TAGTATATATAACTA
5916464 TAGTATATATAACTA
1 TAGTATATATAACTA
5916479 TA
1 TA
5916481 TTAATTTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
TAGTATATATAACTA
Found at i:5916621 original size:61 final size:61
Alignment explanation
Indices: 5916535--5916669 Score: 193
Period size: 61 Copynumber: 2.2 Consensus size: 61
5916525 AAATATATAA
* * * *
5916535 GGATCAAATTGAACAAATTTTAAATATGAAACTTAAATTAATAAATTATAA-CATTACAA-TT
1 GGATTAAATTGAAAAAAGTTGAAATATGAAACTTAAATTAATAAATTA-AATCATTA-AATTT
*
5916596 GGATTAAATTGAAAAAAGTTGAAATATGAAACTTAAATTAATATATTAAATCATTAAATTT
1 GGATTAAATTGAAAAAAGTTGAAATATGAAACTTAAATTAATAAATTAAATCATTAAATTT
5916657 GGATTAAATTGAA
1 GGATTAAATTGAA
5916670 TAAATTTAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
60 4 0.06
61 63 0.94
ACGTcount: A:0.50, C:0.05, G:0.10, T:0.35
Consensus pattern (61 bp):
GGATTAAATTGAAAAAAGTTGAAATATGAAACTTAAATTAATAAATTAAATCATTAAATTT
Found at i:5918033 original size:42 final size:41
Alignment explanation
Indices: 5917987--5918274 Score: 391
Period size: 42 Copynumber: 6.8 Consensus size: 41
5917977 ATTCCAAATT
*
5917987 CGTTGCGA-TAGTCCAAGTTCGCGTTGCGATAGTTC-AAGTTCG
1 CGTTGCGATTATTCCAAGTT--CGTTGCGATAG-TCGAAGTTCG
*
5918029 CGTTGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAGTTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
*
5918071 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
**
5918113 CGTTGCGATTTATTTTAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
* *
5918155 CGTTGCGATTTATTCCAAGTTTGTTGCGATAGTCCAAGTTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
5918197 CGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
1 CGTTGCGA-TTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
*
5918239 CGTTGTGATTTATTCCAAGTTCGCGTTGCGATAGTC
1 CGTTGCGA-TTATTCCAAGTT--CGTTGCGATAGTC
5918275 CAAAATCGCA
Statistics
Matches: 227, Mismatches: 14, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
41 2 0.01
42 202 0.89
44 23 0.10
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.37
Consensus pattern (41 bp):
CGTTGCGATTATTCCAAGTTCGTTGCGATAGTCGAAGTTCG
Found at i:5918170 original size:126 final size:126
Alignment explanation
Indices: 5917998--5918274 Score: 448
Period size: 126 Copynumber: 2.2 Consensus size: 126
5917988 GTTGCGATAG
*
5917998 TCCAAGTTCGCGTTGCGATAGTTCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGTGATAGTC
1 TCCAAGTTC-CGTTGCGATAG-TCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
*
5918063 GAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
64 CAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
** *
5918126 TTTAAGTT-CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTTGTTGCGATAGTCC
1 TCCAAGTTCCGTTGCGATAGTC-AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCC
* *
5918190 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTAT
65 AAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
5918252 TCCAAGTTCGCGTTGCGATAGTC
1 TCCAAGTTC-CGTTGCGATAGTC
5918275 CAAAATCGCA
Statistics
Matches: 137, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
125 2 0.01
126 116 0.85
128 19 0.14
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.37
Consensus pattern (126 bp):
TCCAAGTTCCGTTGCGATAGTCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCCA
AGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
Found at i:5918283 original size:21 final size:21
Alignment explanation
Indices: 5917945--5918277 Score: 276
Period size: 21 Copynumber: 15.8 Consensus size: 21
5917935 TTTTCAAATT
* *
5917945 CGTTGCGATAGTCTAAGTTCA
1 CGTTGCGATAGTCCAAGTTCG
* *
5917966 CGTTGCGATTTATTCCAAATT--
1 CGTTGCGA--TAGTCCAAGTTCG
5917987 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
5918008 CGTTGCGATAGTTCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
5918029 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
* *
5918050 CGTTGTGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
5918071 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
5918092 CGTTGCGATAGTCAAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* **
5918113 CGTTGCGATTTATTTTAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
5918134 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
5918155 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
5918176 TGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
5918197 CGTTGCGATTTATTCCAAGTT--
1 CGTTGCGA--TAGTCCAAGTTCG
*
5918218 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* *
5918239 CGTTGTGATTTATTCCAAGTTCG
1 CGTTGCGA--TAGTCCAAGTTCG
5918262 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
5918278 AATCGCAACG
Statistics
Matches: 251, Mismatches: 35, Indels: 52
0.74 0.10 0.15
Matches are distributed among these distances:
19 54 0.22
21 126 0.50
23 71 0.28
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:5919018 original size:5 final size:5
Alignment explanation
Indices: 5919000--5919034 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
5918990 CTGCCGCCGC
5919000 CGTCT -GTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
5919035 GGTCGTGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 6 0.21
5 22 0.79
ACGTcount: A:0.00, C:0.40, G:0.23, T:0.37
Consensus pattern (5 bp):
CGTCT
Found at i:5919178 original size:21 final size:19
Alignment explanation
Indices: 5919144--5919428 Score: 156
Period size: 19 Copynumber: 13.9 Consensus size: 19
5919134 TCGTTGCGAT
*
5919144 TTTGGATTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
5919163 TTTGGAATAAATCGCAACGTGAA
1 TTTGGAAT--ATCGCAAC--GAA
* * *
5919186 CTTCGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
*
5919205 TTTGTAATAAATCGCAACGCGAA
1 TTTGGAAT--ATCGCAA--CGAA
* * *
5919228 CTTGGACTATCGCAACAAA
1 TTTGGAATATCGCAACGAA
5919247 TTTGGAATAAATCGCAAAGCGAA
1 TTTGGAAT--ATCGC-AA-CGAA
* *
5919270 CTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
*
5919289 TTTGGAAAATCGCAACGCGAA
1 TTTGGAATATCGCAA--CGAA
* *
5919310 CTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
* *
5919329 TTTGGAAAATCGTAACGCGAA
1 TTTGGAATATCGCAA--CGAA
* * * * *
5919350 CTTCGACTATCACAACAAA
1 TTTGGAATATCGCAACGAA
* *
5919369 ATTGGAATAAATCGTAACGCGAA
1 TTTGGAAT--ATCGCAA--CGAA
* * *
5919392 CTTAGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
*
5919411 TTTGGAAAATCGCAACGA
1 TTTGGAATATCGCAACGA
5919429 GAACTTCGAC
Statistics
Matches: 198, Mismatches: 48, Indels: 40
0.69 0.17 0.14
Matches are distributed among these distances:
19 80 0.40
20 2 0.01
21 80 0.40
22 2 0.01
23 34 0.17
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (19 bp):
TTTGGAATATCGCAACGAA
Found at i:5919214 original size:42 final size:41
Alignment explanation
Indices: 5919151--5919448 Score: 395
Period size: 42 Copynumber: 7.2 Consensus size: 41
5919141 GATTTTGGAT
*
5919151 TATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGAC
1 TATCGCAACGAATTT-GAATAAATCGCAACGCGAACTTCGAC
*
5919193 TATCGCAACGAATTTGTAATAAATCGCAACGCGAACTTGGAC
1 TATCGCAACGAATTTG-AATAAATCGCAACGCGAACTTCGAC
* * *
5919235 TATCGCAACAAATTTGGAATAAATCGCAAAGCGAACTTGGAC
1 TATCGCAACGAATTT-GAATAAATCGCAACGCGAACTTCGAC
* *
5919277 TATCGCAACGAATTTGGA-AAATCGCAACGCGAACTTGGAC
1 TATCGCAACGAATTTGAATAAATCGCAACGCGAACTTCGAC
* *
5919317 TATCGCAACGAATTTGGA-AAATCGTAACGCGAACTTCGAC
1 TATCGCAACGAATTTGAATAAATCGCAACGCGAACTTCGAC
* * * * *
5919357 TATCACAACAAAATTGGAATAAATCGTAACGCGAACTTAGAC
1 TATCGCAAC-GAATTTGAATAAATCGCAACGCGAACTTCGAC
* *
5919399 TATCGCAACGAATTTGGA-AAATCGCAACGAGAACTTCGAC
1 TATCGCAACGAATTTGAATAAATCGCAACGCGAACTTCGAC
5919439 TATCGCAACG
1 TATCGCAACG
5919449 CAAACTTAGA
Statistics
Matches: 231, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
40 96 0.42
41 15 0.06
42 119 0.52
43 1 0.00
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (41 bp):
TATCGCAACGAATTTGAATAAATCGCAACGCGAACTTCGAC
Found at i:5919374 original size:122 final size:124
Alignment explanation
Indices: 5919145--5919448 Score: 468
Period size: 122 Copynumber: 2.5 Consensus size: 124
5919135 CGTTGCGATT
* *
5919145 TTGGATTATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGT
1 TTGGACTATCGCAACGAATTTGG-A-AAATCGCAACGAGAACTTCGACTATCGCAACGAATTTGT
* * *
5919210 AATAAATCGCAACGCGAACTTGGACTATCGCAACAAATTTGGAATAAATCGCAAAGCGAAC
64 AATAAATCGCAACGCGAACTTCGACTATCACAACAAAATTGGAATAAATCGCAAAGCGAAC
* * *
5919271 TTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTG-GA
1 TTGGACTATCGCAACGAATTTGGAAAATCGCAACGAGAACTTCGACTATCGCAACGAATTTGTAA
* * *
5919335 -AAATCGTAACGCGAACTTCGACTATCACAACAAAATTGGAATAAATCGTAACGCGAAC
66 TAAATCGCAACGCGAACTTCGACTATCACAACAAAATTGGAATAAATCGCAAAGCGAAC
*
5919393 TTAGACTATCGCAACGAATTTGGAAAATCGCAACGAGAACTTCGACTATCGCAACG
1 TTGGACTATCGCAACGAATTTGGAAAATCGCAACGAGAACTTCGACTATCGCAACG
5919449 CAAACTTAGA
Statistics
Matches: 165, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
122 105 0.64
123 1 0.01
124 36 0.22
125 1 0.01
126 22 0.13
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (124 bp):
TTGGACTATCGCAACGAATTTGGAAAATCGCAACGAGAACTTCGACTATCGCAACGAATTTGTAA
TAAATCGCAACGCGAACTTCGACTATCACAACAAAATTGGAATAAATCGCAAAGCGAAC
Found at i:5919381 original size:82 final size:84
Alignment explanation
Indices: 5919145--5919448 Score: 449
Period size: 82 Copynumber: 3.7 Consensus size: 84
5919135 CGTTGCGATT
* * *
5919145 TTGGATTATCGCAACGAATTTGGAATAAATCGCAACGTGAACTTCGACTATCGCAACGAATTTGT
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG
5919210 AATAAATCGCAACGCGAAC
66 AATAAATCGCAACGCGAAC
* * *
5919229 TTGGACTATCGCAACAAATTTGGAATAAATCGCAAAGCGAACTTGGACTATCGCAACGAATTTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG
5919294 -A-AAATCGCAACGCGAAC
66 AATAAATCGCAACGCGAAC
* * * *
5919311 TTGGACTATCGCAACGAATTTGG-A-AAATCGTAACGCGAACTTCGACTATCACAACAAAATTGG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG
*
5919374 AATAAATCGTAACGCGAAC
66 AATAAATCGCAACGCGAAC
* *
5919393 TTAGACTATCGCAACGAATTTGG-A-AAATCGCAACGAGAACTTCGACTATCGCAACG
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
5919449 CAAACTTAGA
Statistics
Matches: 199, Mismatches: 19, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
80 33 0.17
81 2 0.01
82 104 0.52
83 1 0.01
84 59 0.30
ACGTcount: A:0.37, C:0.21, G:0.19, T:0.22
Consensus pattern (84 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGG
AATAAATCGCAACGCGAAC
Found at i:5919518 original size:21 final size:21
Alignment explanation
Indices: 5919488--5919534 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5919478 TAAATCGTAA
*
5919488 TGCGACAGTCGAAGTTCGCGT
1 TGCGACAGTCGAAGTTCACGT
*
5919509 TGCGATAGTCGAAGTTCACGT
1 TGCGACAGTCGAAGTTCACGT
5919530 TGCGA
1 TGCGA
5919535 ATCTGGAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.26
Consensus pattern (21 bp):
TGCGACAGTCGAAGTTCACGT
Found at i:5921595 original size:16 final size:16
Alignment explanation
Indices: 5921576--5921662 Score: 129
Period size: 16 Copynumber: 5.4 Consensus size: 16
5921566 CAGATCATTT
*
5921576 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTGAAA
5921592 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
* *
5921608 ACATGTCAGGCTGAAA
1 ACAGGTCAGGTTGAAA
5921624 ACAGGTCAGGTTGAAA
1 ACAGGTCAGGTTGAAA
* *
5921640 ACATGTCCGGTTGAAA
1 ACAGGTCAGGTTGAAA
5921656 ACAGGTC
1 ACAGGTC
5921663 GGGTAATACC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 63 1.00
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.20
Consensus pattern (16 bp):
ACAGGTCAGGTTGAAA
Found at i:5922697 original size:29 final size:31
Alignment explanation
Indices: 5922641--5922702 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
5922631 ATGGTTTTGA
* *
5922641 AAAAATTAAAAGTTTAGGTACTAAAACA-AT
1 AAAAACTAAAAGTTTAGATACTAAAACACAT
*
5922671 AAAAACTAATAGTTTAGATACT-AAACACAT
1 AAAAACTAAAAGTTTAGATACTAAAACACAT
5922701 AA
1 AA
5922703 TTTTCCTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 5 0.18
30 23 0.82
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.26
Consensus pattern (31 bp):
AAAAACTAAAAGTTTAGATACTAAAACACAT
Found at i:5924460 original size:14 final size:15
Alignment explanation
Indices: 5924443--5924473 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
5924433 TTCAAAAAAT
5924443 ATTTATTTTTAT-TA
1 ATTTATTTTTATATA
5924457 ATTTATTTTTATATA
1 ATTTATTTTTATATA
5924472 AT
1 AT
5924474 ATTTTATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTATTTTTATATA
Found at i:5924481 original size:18 final size:16
Alignment explanation
Indices: 5924440--5924477 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 16
5924430 TGTTTCAAAA
5924440 AATATTTATTTTTATT
1 AATATTTATTTTTATT
5924456 -A-ATTTATTTTTATAT
1 AATATTTATTTTTAT-T
5924471 AATATTT
1 AATATTT
5924478 TATTAAAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
14 12 0.63
15 2 0.11
16 1 0.05
17 4 0.21
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
AATATTTATTTTTATT
Found at i:5924933 original size:15 final size:15
Alignment explanation
Indices: 5924913--5924944 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
5924903 TTCACAGCCA
5924913 TATTTCGTAAATCAT
1 TATTTCGTAAATCAT
5924928 TATTTCGTAAATCAT
1 TATTTCGTAAATCAT
5924943 TA
1 TA
5924945 AAAAAAGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.06, T:0.47
Consensus pattern (15 bp):
TATTTCGTAAATCAT
Found at i:5933628 original size:35 final size:35
Alignment explanation
Indices: 5933582--5933653 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
5933572 CCAACAAAGA
5933582 AGAGTTGGATTAGGACTCAAATACTAGCCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGCCTAAAAT
*
5933617 AGAGTTGGATTAGGACTCAAATACTAGTCTAAAAT
1 AGAGTTGGATTAGGACTCAAATACTAGCCTAAAAT
5933652 AG
1 AG
5933654 GGTTTTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (35 bp):
AGAGTTGGATTAGGACTCAAATACTAGCCTAAAAT
Found at i:5934240 original size:16 final size:16
Alignment explanation
Indices: 5934219--5934268 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
5934209 TCTTTATAAA
5934219 TTTTTTATTTATTTAT
1 TTTTTTATTTATTTAT
5934235 TTTTTTATTTA-TTACT
1 TTTTTTATTTATTTA-T
* *
5934251 ATTATTATTT-TTTAT
1 TTTTTTATTTATTTAT
5934266 TTT
1 TTT
5934269 AATACTTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
15 6 0.21
16 23 0.79
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTATTTATTTAT
Found at i:5934263 original size:24 final size:25
Alignment explanation
Indices: 5934235--5934282 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
5934225 ATTTATTTAT
*
5934235 TTTTTTA-TTTATTAC-TATTATTA
1 TTTTTTATTTTAATACTTATTATTA
5934258 TTTTTTATTTTAATACTTATTATTA
1 TTTTTTATTTTAATACTTATTATTA
5934283 CTATTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.32
24 7 0.32
25 8 0.36
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTTTATTTTAATACTTATTATTA
Found at i:5934278 original size:31 final size:31
Alignment explanation
Indices: 5934223--5934294 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
5934213 TATAAATTTT
** * *
5934223 TTATTTATTTATTTTTTTATTTATTACTATTA
1 TTATTT-TTTATTTTAATACTTATTACTACTA
*
5934255 TTATTTTTTATTTTAATACTTATTATTACTA
1 TTATTTTTTATTTTAATACTTATTACTACTA
5934286 TTATTTTTT
1 TTATTTTTT
5934295 TGATACCTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
31 29 0.83
32 6 0.17
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (31 bp):
TTATTTTTTATTTTAATACTTATTACTACTA
Found at i:5942397 original size:22 final size:22
Alignment explanation
Indices: 5942369--5942425 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
5942359 TTGAACAGTT
5942369 GAAGAATTCAAGACCAGGGGTC
1 GAAGAATTCAAGACCAGGGGTC
5942391 GAAGAATT-ATAGACCAGGGGTC
1 GAAGAATTCA-AGACCAGGGGTC
*
5942413 GAAAAATTCAAGA
1 GAAGAATTCAAGA
5942426 TTCCAGAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 1 0.03
22 30 0.94
23 1 0.03
ACGTcount: A:0.42, C:0.14, G:0.28, T:0.16
Consensus pattern (22 bp):
GAAGAATTCAAGACCAGGGGTC
Found at i:5943241 original size:106 final size:106
Alignment explanation
Indices: 5943112--5943328 Score: 326
Period size: 106 Copynumber: 2.0 Consensus size: 106
5943102 CAGGCTCAAC
* * * *
5943112 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGATTGTCAACAAACAACTTCCC
* *
5943177 AATTTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
* * *
5943218 ACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGACTGATTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGATTGTCAACAAACAACTTCCC
* * *
5943283 AATTCCAGAGCCAATTTCAACTTCACGGCGGAGGATATTGG
66 AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
5943324 ACTCG
1 ACTCG
5943329 GAGCAACGCA
Statistics
Matches: 99, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
106 99 1.00
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.21
Consensus pattern (106 bp):
ACTCGAGACAACACAAGCTCAACTTCACAACGAAGGGACGACTGATTGTCAACAAACAACTTCCC
AATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
Found at i:5943905 original size:35 final size:35
Alignment explanation
Indices: 5943815--5943884 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
5943805 AACAAAGAAA
*
5943815 AGTTGGATTAGGACTCAAATACTAGTCTAAAATAG
1 AGTTGGATTATGACTCAAATACTAGTCTAAAATAG
5943850 AGTTGGATTATGACTCAAATACTAGTCTAAAATAG
1 AGTTGGATTATGACTCAAATACTAGTCTAAAATAG
5943885 GGTTTTTTAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.30
Consensus pattern (35 bp):
AGTTGGATTATGACTCAAATACTAGTCTAAAATAG
Found at i:5944482 original size:25 final size:25
Alignment explanation
Indices: 5944456--5944511 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
5944446 TAATTTCTTT
*
5944456 TTTTA-TTTATTAC-TATTATTATC
1 TTTTATTTTAATACTTATTATTATC
5944479 TTTTATTTTAATACTTATTATTA-C
1 TTTTATTTTAATACTTATTATTATC
*
5944503 TATTATTTT
1 TTTTATTTT
5944512 TTTATACCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 5 0.17
24 16 0.55
25 8 0.28
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (25 bp):
TTTTATTTTAATACTTATTATTATC
Found at i:5944542 original size:2 final size:2
Alignment explanation
Indices: 5944535--5944577 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5944525 TATAAGTTGT
5944535 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5944577 T
1 T
5944578 TCATATAACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.